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1.
BMC Infect Dis ; 19(1): 677, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31370796

RESUMO

BACKGROUND: In this study, the association between high-risk human papillomavirus (hrHPV) infection and the vaginal microbiome in pregnant women was evaluated in Chinese cohorts. METHODS: The vaginal bacterial composition of four groups, 38 hrHPV-infected pregnant women (PHR, n = 38), pregnant women without HPV infection (PN, n = 48), nonpregnant women with hrHPV infection (NPHR, n = 19) and nonpregnant women without HPV infection (NPN, n = 30), was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V3-4) using Illumina MiSeq. RESULTS: The results revealed that both pregnancy and HPV infection can increase vaginal bacterial microbial richness and diversity, with the bacterial composition being most influenced by pregnancy. Lactobacillus was the most dominant genus among all samples. NPN samples were dominated by CST (community state type) III, mainly composed of Lactobacillus iners. Both pregnancy and hrHPV infection were accompanied by an increased proportion of CST I (dominated by Lactobacillus crispatus), as opposed to CST III. Bifidobacterium, Bacillus, Megasphaera, Sneathia, Prevotella, Gardnerella, Fastidiosipila and Dialister were found to be biomarkers for hrHPV-infected women, though different genera (Bifidobacterium, Megasphaera, Bacillus, Acidovorax, Oceanobacillus and Lactococcus) were associated with hrHPV-infected pregnant women. CONCLUSIONS: This work uncovered a probable synergistic effect of hrHPV infection and pregnancy on the vaginal microbial composition. HPV infection in pregnant women was associated with a more complex and diverse microbial environment.


Assuntos
Microbiota , Infecções por Papillomavirus/microbiologia , Vagina/microbiologia , Vagina/virologia , Adulto , Grupo com Ancestrais do Continente Asiático , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Microbiota/genética , Infecções por Papillomavirus/virologia , Gravidez , RNA Ribossômico 16S/genética
2.
Genome Biol ; 20(1): 153, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375138

RESUMO

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.


Assuntos
Resistência Microbiana a Medicamentos/genética , Metagenômica/métodos , Microbiota/genética , Análise de Sequência de DNA/métodos , Vírus/genética , Animais , Bovinos , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Transferência Genética Horizontal , Genes Microbianos , Fases de Leitura Aberta , Prófagos/genética , Rúmen/microbiologia , Rúmen/virologia , Vírus/isolamento & purificação
3.
Genome Biol ; 20(1): 154, 2019 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-31387630

RESUMO

We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show that including reads from unknown organisms significantly increases the prediction accuracy of the disease status for three of the four datasets. We identify new microbial organisms associated with these diseases and show viruses play important prediction roles in colorectal cancer and liver cirrhosis, but not in type 2 diabetes. MicroPro is freely available at https://github.com/zifanzhu/MicroPro .


Assuntos
Doença , Metagenômica/métodos , Microbiota/genética , Software , Fenômenos Fisiológicos Virais , Neoplasias Colorretais/virologia , Diabetes Mellitus Tipo 2/virologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cirrose Hepática/virologia
4.
Microbiol Res ; 226: 65-73, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284946

RESUMO

Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.


Assuntos
Bactérias/classificação , Biodiversidade , Ecossistema , Microbiota , Água do Mar/microbiologia , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Ecologia , Sedimentos Geológicos/microbiologia , Índia , Biologia Marinha , Microbiota/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência
5.
Ecotoxicol Environ Saf ; 182: 109452, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31351330

RESUMO

Antimicrobial resistance gene (ARG) abundance and microbial resistance (MR) are often used as important indicators of pollution risk; however, the relationship between ARGs abundance and MR in pig farm wastewater remains unknown. In this study, the raw pig farm wastewater, effluent water, upstream river water, domestic wastewater and downstream river water samples were collected. The concentration of 20 subtypes of ARGs and 2 integrons, minimal inhibit concentration (MIC), and bacterial communities were investigated. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. The highest abundance of 17 of the 20 subtypes of ARGs was detected in raw pig farm wastewater, and ermA had the maximum average abundance of 108 copies/mL, with up to 2.41 ±â€¯0.12 × 108 copies/mL. There was no significant correlation between MR to three antibiotics (ciprofloxacin, streptomycin and tetracycline hydrochloride) and the abundance of their corresponding ARGs (P > 0.05), and a large difference was detected between the types of ARGs co-occur bacteria and resistance co-occur bacteria in the 5 sampling sites. And the pig farm wastewater treatment (WWT) could effectively reduce the ARGs and MR to the 3 antibiotics. The results presented here show that there may be no obvious correlation between ARGs and MCR in pig farm wastewater and surrounding rivers, which may be due to various environmental factors, highlighting the urgent need for a comprehensive evaluation of relationship between ARGs abundance and MR.


Assuntos
Antibacterianos/análise , Farmacorresistência Bacteriana/efeitos dos fármacos , Genes Bacterianos , Microbiota/efeitos dos fármacos , Rios/microbiologia , Águas Residuárias/microbiologia , Poluentes Químicos da Água/análise , Animais , Farmacorresistência Bacteriana/genética , Fazendas , Integrons/efeitos dos fármacos , Integrons/genética , Microbiota/genética , Rios/química , Suínos , Águas Residuárias/química
6.
Nat Commun ; 10(1): 3066, 2019 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-31296857

RESUMO

Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves >94% accuracy for species-level read assignment and r2 > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes.


Assuntos
Biologia Computacional/métodos , Análise de Dados , Metagenômica/métodos , Algoritmos , Conjuntos de Dados como Assunto , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenoma/genética , Microbiota/genética , Análise de Sequência de DNA/métodos , Software
7.
Mar Pollut Bull ; 142: 169-177, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31232291

RESUMO

Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.


Assuntos
Sedimentos Geológicos/microbiologia , Microbiota/fisiologia , Campos de Petróleo e Gás/microbiologia , Biodiversidade , Monitoramento Ambiental/métodos , Sedimentos Geológicos/química , Halomonas/genética , Halomonas/metabolismo , Hidrocarbonetos/metabolismo , Microbiota/genética , Mar do Norte
8.
BMC Bioinformatics ; 20(Suppl 12): 314, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31216991

RESUMO

BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in healthy and sick individuals for a variety of diseases; this suggests that the microbiome profile can be used as a diagnostic tool in identifying the disease states of an individual. However, the high-dimensional nature of metagenomic data poses a significant challenge to existing machine learning models. Consequently, to enable personalized treatments, an efficient framework that can accurately and robustly differentiate between healthy and sick microbiome profiles is needed. RESULTS: In this paper, we propose MetaNN (i.e., classification of host phenotypes from Metagenomic data using Neural Networks), a neural network framework which utilizes a new data augmentation technique to mitigate the effects of data over-fitting. CONCLUSIONS: We show that MetaNN outperforms existing state-of-the-art models in terms of classification accuracy for both synthetic and real metagenomic data. These results pave the way towards developing personalized treatments for microbiome related diseases.


Assuntos
Algoritmos , Metagenômica/métodos , Redes Neurais (Computação) , Área Sob a Curva , Bases de Dados Genéticas , Humanos , Aprendizado de Máquina , Microbiota/genética , Modelos Teóricos , Fenótipo , Curva ROC , Máquina de Vetores de Suporte
10.
J Med Microbiol ; 68(8): 1148-1158, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31199220

RESUMO

PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes. METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument. RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves. CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.


Assuntos
Microbiota , Boca/microbiologia , Fumar , Adulto , Bactérias/classificação , Bactérias/genética , Feminino , Genoma Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Adulto Jovem
11.
World J Microbiol Biotechnol ; 35(7): 100, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31222403

RESUMO

The spontaneously fermented curdled milk product from Burkina Faso, lait caillé is prepared by traditional processing from raw unpasteurised milk. The fermentation lasts 1-3 days. This study aims to identify the predominant microbiota involved in lait caillé fermentation from cow milk. A survey on lait caillé end-products from local markets showed pH ranges of 3.5 to 4.2. Counts of total lactic acid bacteria (LAB) were 7.8 ± 0.06 to 10.0 ± 0.03 log CFU/g and yeast counts were 5.3 ± 0.06 to 8.7 ± 0.01 log CFU/g, together with considerate amounts of Enterobacteriaceae < 3.00 to 8.4 ± 0.14 log CFU/g. Sampling throughout the entire fermentation of lait caillé was performed at a traditional house-hold production site. A drop in pH from 6.7 ± 0.01 at 0 h to 4.3 ± 0.08 in the end-product (59 h) was found. Total LAB counts increased to 8.6 ± 0.02 log CFU/g in the end-product, while yeast and Enterobacteriaceae counts reached 6.4 ± 0.11 and 6.7 ± 0.00 log CFU/g, respectively. LAB and yeasts isolated during the fermentation were clustered by (GTG)5 repetitive-PCR fingerprinting followed by 16S and 26S rRNA gene sequencing, respectively. Microbial successions were observed with Leuconostoc mesenteroides being the predominant LAB followed by Pediococcus pentosaceus and Weissella paramesenteroides at the onset, while Lactococcus lactis and Enterococcus spp. where the predominant LAB after 7 h of fermentation. During the first 18 h Candida parapsilosis was the dominant yeast species, while from 35 h to the end-product, Saccharomyces cerevisiae predominated. The microbial safety risk pointed out in this study, showed the need for implementation of good manufacturing practices including pasteurisation and use of well-defined starter cultures.


Assuntos
Produtos Fermentados do Leite/microbiologia , Microbiota/genética , Burkina Faso , Contagem de Colônia Microbiana , Enterobacteriaceae/genética , Enterobacteriaceae/isolamento & purificação , Enterococcus/genética , Enterococcus/isolamento & purificação , Fermentação , Manipulação de Alimentos , Microbiologia de Alimentos , Concentração de Íons de Hidrogênio , Lactobacillales/genética , Lactobacillales/isolamento & purificação , Lactococcus lactis/genética , Lactococcus lactis/isolamento & purificação , RNA Ribossômico/genética , RNA Ribossômico/isolamento & purificação , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de RNA , Leveduras/genética , Leveduras/isolamento & purificação
12.
World J Microbiol Biotechnol ; 35(7): 104, 2019 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-31236765

RESUMO

Endophytic bacterial diversity in plants presents the level of interaction between culturable and non-culturable endophytic bacteria, thereby providing an appropriate insight into the endophytic environment. This study was conducted to determine the trend of culturable and non-culturable endophytic bacteria at two different sites encompassing four consecutive growth stages. For culturable endophytic bacteria, isolation was carried out using the dilution plate technique, and the obtained colonies were compared using PCR-restriction fragment length polymorphism (RFLP). Different RFLP-types were identified to their nearest neighbour using 16S rRNA sequencing. The non-culturable endophytic bacterial diversity was obtained by next generation sequencing. Results suggested a similar trend among the culturable and non-culturable bacteria for observed operational taxonomic units and diversity indices. It is noticeable that the endophytic bacteria inhabiting in stage 1 disappeared, and instead, different endophytic bacteria appeared. Moreover, the temporal persistence of certain culturable and non-culturable bacteria was also observed. In conclusion, the endophytic bacterial diversity in cucumber initially increased with the plant growth and then decreased at a later stage. Furthermore, it was suggested that plants regulate the number and diversity of endophytes throughout the lifecycle of plants.


Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Biodiversidade , Cucumis sativus/microbiologia , Endófitos/classificação , Endófitos/isolamento & purificação , Microbiota , Bactérias/genética , Cucumis sativus/crescimento & desenvolvimento , DNA Bacteriano/análise , DNA Bacteriano/isolamento & purificação , Endófitos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota/genética , Filogenia , Raízes de Plantas/microbiologia , Reação em Cadeia da Polimerase/métodos , Polimorfismo de Fragmento de Restrição , RNA Ribossômico 16S/genética
13.
Syst Appl Microbiol ; 42(4): 481-487, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31153679

RESUMO

Biogas plants achieve its highest yield on plant biomass only with the most efficient hydrolysis of cellulose. This is driven by highly specialized hydrolytic microorganisms, which we have analyzed by investigating enrichment strategies for the isolation of cellulolytic bacteria out of a lab-scale biogas fermenter. We compared three different cultivation media as well as two different inoculation materials: Enrichment on filter paper in nylon bags (in sacco) or raw digestate. Next generation sequencing of the V3/V4 region of the bacterial 16S rRNA of metagenomic DNA from six different enrichment cultures, each in biological triplicates, revealed an average richness of 48 different OTU's with an average evenness of 0.3 in each sample. ß-Diversity of the bacterial community revealed significant differences between the two sampling techniques or the different media used. The isolation attempt of single cellulolytic organisms resulted in several clonal pure cultures. Regardless which medium or inoculation material, well-known cellulolytic key players such as Clostridium cellulosi, Herbinix hemicellulosilytica and Hungateiclostridium thermocellum were among the isolates. The inoculation material as well as the cultivation conditions are crucial to cultivate the representative cellulolytic organisms. Taking raw digestate as inoculation material and using the same material, filtered and sterilized, for supplementing media allowed to imitate the natural habitat. Pre-enrichment of cellulolytic organisms directly in their natural habitat led to significant advantages concerning high diversity and high abundance of unknown cellulolytic organisms, which is a key factor for the isolation of hitherto unknown species.


Assuntos
Biocombustíveis/microbiologia , Celulose/metabolismo , Microbiologia Industrial/métodos , Microbiota , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biodiversidade , Biomassa , Reatores Biológicos/microbiologia , Meios de Cultura , DNA Bacteriano/genética , Metagenoma , Microbiota/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
14.
BMC Bioinformatics ; 20(Suppl 11): 276, 2019 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-31167633

RESUMO

BACKGROUND: A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and searched against reference databases, or individually searched without assembly. The first approach may suffer from fragmentary and incomplete assembly, while the second is hampered by the reduced functional signal contained in the short reads. To tackle these issues, we have previously developed GRASP (Guided Reference-based Assembly of Short Peptides), which accepts a reference protein sequence as input and aims to assemble its homologs from a database containing fragmentary protein sequences. In addition to a gene-centric assembly tool, GRASP also serves as a homolog search tool when using the assembled protein sequences as templates to recruit reads. GRASP has significantly improved recall rate (60-80% vs. 30-40%) compared to other homolog search tools such as BLAST. However, GRASP is both time- and space-consuming. Subsequently, we developed GRASPx, which is 30X faster than GRASP. Here, we present a completely redesigned algorithm, GRASP2, for this computational problem. RESULTS: GRASP2 utilizes Burrows-Wheeler Transformation (BWT) and FM-index to perform assembly graph generation, and reduces the search space by employing a fast ungapped alignment strategy as a filter. GRASP2 also explicitly generates candidate paths prior to alignment, which effectively uncouples the iterative access of the assembly graph and alignment matrix. This strategy makes the execution of the program more efficient under current computer architecture, and contributes to GRASP2's speedup. GRASP2 is 8-fold faster than GRASPx (and 250-fold faster than GRASP) and uses 8-fold less memory while maintaining the original high recall rate of GRASP. GRASP2 reaches ~ 80% recall rate compared to that of ~ 40% generated by BLAST, both at a high precision level (> 95%). With such a high performance, GRASP2 is only ~3X slower than BLASTP. CONCLUSION: GRASP2 is a high-performance gene-centric and homolog search tool with significant speedup compared to its predecessors, which makes GRASP2 a useful tool for metagenomics data analysis, GRASP2 is implemented in C++ and is freely available from http://www.sourceforge.net/projects/grasp2 .


Assuntos
Genes , Metagenômica/métodos , Análise de Sequência de DNA/métodos , Homologia de Sequência do Ácido Nucleico , Software , Algoritmos , Organismos Aquáticos/genética , Microbiota/genética , Curva ROC , Fatores de Tempo
15.
J Microbiol Biotechnol ; 29(7): 1104-1116, 2019 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-31216610

RESUMO

In this study, we investigated the potential of using sediment bioelectrochemical systems (SBESs) for in situ treatment of the water and sediment in brackish aquaculture ponds polluted with uneaten feed. An SBES integrated into a laboratory-scale tank simulating a brackish aquaculture pond was established. This test tank and the control (not containing the SBES) were fed with shrimp feed in a scheme that mimics a situation where 50% of feed is uneaten. After the SBES was inoculated with microbial sources from actual shrimp pond sediments, electricity generation was well observed from the first experimental week, indicating successful enrichment of electrochemically active bacteria in the test tank sediment. The electricity generation became steady after 3 weeks of operation, with an average current density of 2.3 mA/m2 anode surface and an average power density of 0.05 mW/m2 anode surface. The SBES removed 20-30% more COD of the tank water, compared to the control. After 1 year, the SBES also reduced the amount of sediment in the tank by 40% and thus could remove approximately 40% more COD and approximately 52% more nitrogen from the sediment, compared to the control. Insignificant amounts of nitrite and nitrate were detected, suggesting complete removal of nitrogen by the system. PCR-DGGE-based analyses revealed the dominant presence of Methylophilus rhizosphaerae, Desulfatitalea tepidiphila and Thiothrix eikelboomii, which have not been found in bioelectrochemical systems before, in the bacterial community in the sediment of the SBES-containing tank. The results of this research demonstrate the potential application of SBESs in helping to reduce water pollution threats, fish and shrimp disease risks, and thus farmers' losses.


Assuntos
Aquicultura , Microbiota , Tanques/microbiologia , Eliminação de Resíduos Líquidos/métodos , Poluentes da Água/metabolismo , Ração Animal , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodegradação Ambiental , Fontes de Energia Bioelétrica , Análise da Demanda Biológica de Oxigênio , Eletricidade , Sedimentos Geológicos/química , Sedimentos Geológicos/microbiologia , Microbiota/genética , Nitrogênio/análise , Tanques/química
16.
Ecotoxicol Environ Saf ; 180: 705-714, 2019 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-31151067

RESUMO

Heavy metals and polybrominated diphenyl ethers (PBDEs) are ubiquitous pollutants at electronic waste (e-waste) contaminated sites, their individual impacts on soil microbial community has attracted wide attention, however, limited research is available on the combined effects of heavy metals and PBDEs on microbial community of e-waste contaminated. Therefore, combined effects of heavy metals and PBDEs on the microbial community in the e-waste contaminated soil were investigated in this study. Samples were collected from Ziya e-waste recycling area in Tianjin, northern China, and the soil microbial communities were then analyzed by the high-throughput MiSeq 16S rRNA sequencing to assess the effects of soil properties, heavy metals, and PBDEs on the soil microbial community. Candidatus Nitrososphaera, Steroidobacter and Kaistobacter were the dominant microbial species in the soils. Similar microbial metabolic functions, including amino acid metabolism, carbohydrate metabolism and membrane transport, were found in all soil samples. Redundancy analysis and variation partition analysis revealed that the microbial community was mainly influenced by PBDEs (including BDE 183, BDE 99, BDE 100 and BDE 154) in horizontal soil samples. However, TN, biomass, BDE 100, BDE 99 and BDE 66 were the major drivers shaping the microbial community in vertical soil samples.


Assuntos
Resíduo Eletrônico , Éteres Difenil Halogenados/toxicidade , Metais Pesados/toxicidade , Microbiota/efeitos dos fármacos , Microbiologia do Solo , China , Resíduo Eletrônico/análise , Monitoramento Ambiental , Éteres Difenil Halogenados/análise , Metais Pesados/análise , Microbiota/genética , Microbiota/fisiologia , RNA Ribossômico 16S/genética , Solo/química , Poluentes do Solo/análise , Poluentes do Solo/toxicidade
17.
Nat Commun ; 10(1): 2719, 2019 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-31222023

RESUMO

Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. Here, we demonstrate common pitfalls in comparing relative abundance across samples and identify two solutions that reveal microbial changes without the need to estimate total microbial load. We define the notion of "reference frames", which provide deep intuition about the compositional nature of microbiome data. In an oral time series experiment, reference frames alleviate false positives and produce consistent results on both raw and cell-count normalized data. Furthermore, reference frames identify consistent, differentially abundant microbes previously undetected in two independent published datasets from subjects with atopic dermatitis. These methods allow reassessment of published relative abundance data to reveal reproducible microbial changes from standard sequencing output without the need for new assays.


Assuntos
Bactérias/isolamento & purificação , Análise de Dados , Microbiota/genética , Modelos Biológicos , Bactérias/genética , Carga Bacteriana/normas , Simulação por Computador/normas , Conjuntos de Dados como Assunto , Dermatite Atópica/microbiologia , Estudos de Viabilidade , Voluntários Saudáveis , Sequenciamento de Nucleotídeos em Larga Escala/estatística & dados numéricos , Humanos , Metagenoma/genética , RNA Ribossômico 16S/isolamento & purificação , Padrões de Referência , Saliva/microbiologia , Microbiologia do Solo
18.
Food Microbiol ; 83: 48-58, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31202418

RESUMO

The various stages of the cheese-making process harbor distinct bacterial communities which may influence the sensory characteristics of artisanal cheeses. The objective of this study was to investigate the microbiota from dairy farm to final cheeses along an artisanal cheese-making continuum. Environmental and food samples were collected from 21 sites, including the dairy farm, milk, cheese plant, and finished cheeses. The microbiota of these samples were analyzed using 16S rRNA amplicon sequencing, with sequences grouped into operational taxonomic units (OTUs) by phylotype at the genus level. Alpha diversity decreased from dairy farm to finished cheese. Firmicutes was the dominant phylum, ranging from 31% to 92% between the dairy farm and finished cheeses, respectively, with Proteobacteria, Actinobacteria, and Bacteroides also present (25%, 11%, and 9% overall relative abundance, respectively). Of the 37 core OTUs (>5 reads in >80% of site replicates) observed in cheese, 32 were shared with the dairy farm. Starter-related genera (i.e., Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc) represented between 69% and 98% relative abundance in final cheeses depending on style, with the remainder likely acquired from various environmental sources on the farm and during the cheese-making process.


Assuntos
Bactérias/classificação , Queijo/microbiologia , Fazendas , Microbiota/genética , Leite/microbiologia , Animais , Bactérias/isolamento & purificação , DNA Bacteriano/genética , Indústria de Laticínios , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , RNA Ribossômico 16S/genética
19.
BMC Biol ; 17(1): 45, 2019 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146755

RESUMO

BACKGROUND: Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. RESULTS: We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. CONCLUSIONS: Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.


Assuntos
Arsênico/efeitos adversos , Bactérias/efeitos dos fármacos , Farmacorresistência Bacteriana/genética , Microbiota/efeitos dos fármacos , Microbiologia do Solo , Poluentes do Solo/efeitos adversos , Acesso à Informação , Arsênico/metabolismo , Bactérias/genética , Bactérias/metabolismo , Microbiota/genética
20.
BMC Biol ; 17(1): 48, 2019 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-31189463

RESUMO

Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered using metagenomics, but different kinds of "unknowns" still remain in a microbiome experiment. We discuss here whether and how it is possible to deal with them.


Assuntos
Metagenoma , Metagenômica , Microbiota , Archaea/classificação , Archaea/fisiologia , Bactérias/classificação , Fenômenos Fisiológicos Bacterianos , Microbiota/genética
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