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1.
Chemosphere ; 247: 125925, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32069717

RESUMO

Environmental pollutants could change the intestinal microbiota communities, while data concerning the dynamics of the intestinal microbiota in response to different environmental chemicals in amphibian are lacking. We compared the effects of Cu, Cd, Cr and NO3-N on intestinal microbiota of B. gargarizans tadpoles by using high-throughput 16S rRNA sequencing technology. Our results revealed that responses of intestinal microbiota to three metals and NO3-N showed different characteristics. At the phylum level, the most 100 OTUs were predominantly colonized by Proteobacteria, and meanwhile, expansion of Proteobacteria was observed in Cu 64 µg/L, Cd (100 µg/L and 200 µg/L) and NO3-N100 mg/L treatment groups. In addition, the abundance of Bacteroidetes significantly increased in the gut administrate with Cu, Cd, Cr, NO3-N 20 mg/L exposures, while declined abundance of Fusobacteria was observed in Cu64 µg/L Cd100 µg/L Cd200µg/L-exposed groups. At the genus level, several genera exhibited increased prevalence of abundance such as Shewanella, Azospira and Flavobacterium. The functional prediction revealed that exposures of three metals and NO3-N increase the risks of metabolic disorders and diseases. Our research could be an important step toward an assessment of the ecological risks of different chemicals to aquatic organisms using intestinal microbiota.


Assuntos
Bufonidae/microbiologia , Poluentes Ambientais/toxicidade , Microbioma Gastrointestinal/efeitos dos fármacos , Animais , Bacteroidetes/genética , Bufonidae/genética , Cádmio/farmacologia , Microbioma Gastrointestinal/fisiologia , Larva/efeitos dos fármacos , Metais/toxicidade , Nitratos/toxicidade , RNA Ribossômico 16S/genética
2.
PLoS One ; 15(2): e0228133, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32023276

RESUMO

The neonatal period, during which the initial gut microbiota is acquired, is a critical phase. The healthy development of the infant's microbiome can be interrupted by external perturbations, like antibiotics, which are associated with profound effects on the gut microbiome and various disorders later in life. The aim of this study was to investigate the development of intestinal microbiota and the effect of antibiotic exposure during the first three months of life in term infants. Fecal samples were collected from healthy infants and infants who received antibiotics in the first week of life at one week, one month, and three months after birth. Microbial composition was analyzed using IS-pro and compared between antibiotics-treated and untreated infants. In total, 98 infants, divided into four groups based on feeding type and delivery mode, were analyzed. At one week of age, samples clustered into two distinct groups, which were termed "settler types", based on their Bacteroidetes abundance. Caesarean-born infants belonged to the low-Bacteroidetes settler type, but vaginally-born infants were divided between the two groups. The antibiotics effect was assessed within a subgroup of 45 infants, vaginally-born and exclusively breastfed, to minimize the effect of other confounders. Antibiotics administration resulted in lower Bacteroidetes diversity and/or a delay in Bacteroidetes colonization, which persisted for three months, and in a differential development of the microbiota. Antibiotics resulted in pronounced effects on the Bacteroidetes composition and dynamics. Finally, we hypothesize that stratification of children's cohorts based on settler types may reveal group effects that might otherwise be masked.


Assuntos
Antibacterianos/farmacologia , Microbioma Gastrointestinal/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , DNA Bacteriano/isolamento & purificação , DNA Bacteriano/metabolismo , Fezes/microbiologia , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Análise de Componente Principal , RNA Ribossômico 16S/isolamento & purificação , RNA Ribossômico 16S/metabolismo
3.
Syst Appl Microbiol ; 43(2): 126065, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32057584

RESUMO

To date, the phylum Bacteroidetes comprises more than 1,500 described species with diverse ecological roles. However, there is little understanding of archetypal Bacteroidetes traits at a genomic level. In this study, a representative set of 89 Bacteroidetes genomes was compiled, and pairwise reciprocal best-match gene comparisons and gene syntenies were used to identify common traits that allowed Bacteroidetes evolution and adaptive radiation to be traced. The type IX secretion system (T9SS) was highly conserved among all studied Bacteroidetes. Class-level comparisons furthermore suggested that the ACIII-caa3COX super-complex evolved in the ancestral aerobic bacteroidetal lineage, and was secondarily lost in extant anaerobic Bacteroidetes. Another Bacteroidetes-specific respiratory chain adaptation was the sodium-pumping Nqr complex I that replaced the ancestral proton-pumping complex I in marine species. T9SS plays a role in gliding motility and the acquisition of complex macro-molecular organic compounds, and the ACIII-caa3COX super-complex allows effective control of electron flux during respiration. This combination likely provided ancestral Bacteroidetes with a decisive competitive advantage to effectively scavenge, uptake and degrade complex organic molecules, and therefore has played a pivotal role in the successful adaptive radiation of the phylum.


Assuntos
Adaptação Fisiológica/genética , Bacteroidetes/genética , Evolução Molecular , Genoma Bacteriano/genética , Proteínas de Bactérias/genética , Sistemas de Secreção Bacterianos/genética , Bacteroidetes/classificação , Bacteroidetes/fisiologia , Transporte de Elétrons/genética , Locomoção/genética , Filogenia
4.
World J Microbiol Biotechnol ; 36(2): 29, 2020 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-32016527

RESUMO

Short-chain halogenated aliphatic hydrocarbons (e.g. perchloroethene, trichloroethene) are among the most toxic environmental pollutants. Perchloroethene and trichloroethene can be dechlorinated to non-toxic ethene through reductive dechlorination by Dehalococcoides sp. Bioaugmentation, applying cultures containing organohalide-respiring microorganisms, is a possible technique to remediate sites contaminated with chlorinated ethenes. Application of site specific inocula is an efficient alternative solution. Our aim was to develop site specific dechlorinating microbial inocula by enriching microbial consortia from groundwater contaminated with trichloroethene using microcosm experiments containing clay mineral as solid phase. Our main goal was to develop fast and reliable method to produce large amount (100 L) of bioactive agent with anaerobic fermentation technology. Polyphasic approach has been applied to monitor the effectiveness of dechlorination during the transfer process from bench-scale (500 mL) to industrial-scale (100 L). Gas chromatography measurement and T-RFLP (Terminal Restriction Fragment Length Polymorphism) revealed that the serial subculture of the enrichments shortened the time-course of the complete dechlorination of trichloroethene to ethene and altered the composition of bacterial communities. Complete dechlorination was observed in enrichments with significant abundance of Dehalococcoides sp. cultivated at 8 °C. Consortia incubated in fermenters at 18 °C accelerated the conversion of TCE to ethene by 7-14 days. Members of the enrichments belong to the phyla Bacteroidetes, Chloroflexi, Proteobacteria and Firmicutes. According to the operational taxonomic units, main differences between the composition of the enrichment incubated at 8 °C and 18 °C occurred with relative abundance of acetogenic and fermentative species. In addition to the temperature, the site-specific origin of the microbial communities and the solid phase applied during the fermentation technique contributed to the development of a unique microbial composition.


Assuntos
Anaerobiose/fisiologia , Bactérias/metabolismo , Biodegradação Ambiental , Argila/química , Microbiota/fisiologia , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteroidetes/genética , Bacteroidetes/metabolismo , Chloroflexi/genética , Chloroflexi/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Fermentação , Firmicutes/genética , Firmicutes/metabolismo , Geobacter/genética , Geobacter/metabolismo , Água Subterrânea/microbiologia , Consórcios Microbianos , Polimorfismo de Fragmento de Restrição , Proteobactérias/genética , Proteobactérias/metabolismo , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/isolamento & purificação , Tricloroetileno/química , Microbiologia da Água , Poluentes Químicos da Água/metabolismo
5.
PLoS One ; 15(1): e0227886, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31978162

RESUMO

BACKGROUND: Microbial communities of the mouse gut have been extensively studied; however, their functional roles and regulation are yet to be elucidated. Metagenomic and metatranscriptomic analyses may allow us a comprehensive profiling of bacterial composition and functions of the complex gut microbiota. The present study aimed to investigate the active functions of the microbial communities in the murine cecum by analyzing both metagenomic and metatranscriptomic data on specific bacterial species within the microbial communities, in addition to the whole microbiome. RESULTS: Bacterial composition of the healthy mouse gut microbiome was profiled using the following three different approaches: 16S rRNA-based profiling based on amplicon and shotgun sequencing data, and genome-based profiling based on shotgun sequencing data. Consistently, Bacteroidetes, Firmicutes, and Deferribacteres emerged as the major phyla. Based on NCBI taxonomy, Muribaculaceae, Lachnospiraceae, and Deferribacteraceae were the predominant families identified in each phylum. The genes for carbohydrate metabolism were upregulated in Muribaculaceae, while genes for cofactors and vitamin metabolism and amino acid metabolism were upregulated in Deferribacteraceae. The genes for translation were commonly enhanced in all three families. Notably, combined analysis of metagenomic and metatranscriptomic sequencing data revealed that the functions of translation and metabolism were largely upregulated in all three families in the mouse gut environment. The ratio of the genes in the metagenome and their expression in the metatranscriptome indicated higher expression of carbohydrate metabolism in Muribaculum, Duncaniella, and Mucispirillum. CONCLUSIONS: We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metatranscriptomic data, we found that the expression rates differed for different functional categories in the mouse gut environment. Application of these methods to track microbial transcription in individuals over time, or before and after administration of a specific stimulus will significantly facilitate future development of diagnostics and treatments.


Assuntos
Bactérias/genética , Microbioma Gastrointestinal/genética , Metagenoma/genética , Metagenômica , Animais , Bactérias/classificação , Bacteroidetes/genética , Fezes/microbiologia , Firmicutes/genética , Camundongos , Microbiota/genética , RNA Ribossômico 16S/genética , Transcriptoma/genética
6.
PLoS One ; 15(1): e0227864, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31990915

RESUMO

The type VI secretion system (T6SS) is a nanomachine capable of killing adjacent microbial cells in a contact-dependent manner. Due to limited studies, relatively little is known about the range of marine bacteria that are susceptible to T6SS attack. Here, 15 diverse marine bacterial isolates from the phyla Bacteroidetes and Ɣ-Proteobacteria were challenged against the marine bacterium and human pathogen, Vibrio cholerae, which has a well described T6SS. V. cholerae killed several of the tested Ɣ-Proteobacteria, including members of the orders Vibrionales, Alteromonadales, Oceanospirillales, and Pseudomonadales. In contrast, V. cholerae co-existed with multiple Bacteroidetes and Ɣ-Proteobacteria isolates, but was killed by Vibrio coralliilyticus. Follow-up experiments revealed that five V. coralliilyticus strains, including known coral and shellfish pathogens survived the T6SS challenge and killed V. cholerae. By using predicted protein comparisons and mutagenesis, we conclude that V. coralliilyticus protected itself in the challenge by using its own T6SS to kill V. cholerae. This study provides valuable insight into the resilience and susceptibility of marine bacteria to the V. cholerae T6SS, and provides the first evidence for a functional T6SS in V. coralliilyticus, both of which have implications for human and ocean health.


Assuntos
Sistemas de Secreção Tipo VI/genética , Vibrio cholerae/patogenicidade , Vibrio/genética , Animais , Antozoários/microbiologia , Anticorpos Antibacterianos/genética , Proteínas de Bactérias/genética , Bacteroidetes/genética , Regulação Bacteriana da Expressão Gênica/genética , Proteobactérias/genética , Frutos do Mar/microbiologia , Vibrio cholerae/genética
7.
Arch Microbiol ; 202(1): 127-134, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31515591

RESUMO

A novel bacterial strain, designated ZR32T, was isolated from briquette warehouse soil in Ulsan (Korea). The strain was aerobic, showing pink-colored colonies on R2A agar. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZR32T was closely related to Mucilaginibacter soli R9-65T (97.0%), Mucilaginibacter gynuensis YC7003T (96.9%), and Mucilaginibacter lutimaris BR-3T (96.8%). The values of DNA-DNA relatedness related two highest strains M. soli R9-65T and M. gynuensis YC7003T were 31.2 ± 6.9% and 19.7 ± 0.3%, respectively. Its genome size was 3.9 Mb, comprising 3402 predicted genes. The DNA G+C content of strain ZR32T was 43.0 mol%. The major cellular fatty acids (> 5% of total) were summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0, C16:1ω5c, iso-C15:0, iso-C17:0 3-OH, and C17:1ω9c. The major respiratory quinine was menaquinone-7 (MK-7). The major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, one unidentified sphingolipid, and one unidentified polar lipid. Strain ZR32T showed distinctive characteristics such as the temperature and pH for growth ranges, being positive for ß-glucosidase, salicin production, negative for N-acetyl-glucosamine assimilation, being resistant to carbenicillin and piperacillin to related species. On the basis of phenotypic, chemotaxonomic, and phylogenetic data, strain ZR32T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter hurinus sp. nov. is proposed. The type strain is ZR32T (= KCTC 62193 = CCTCC AB 2017285).


Assuntos
Bacteroidetes/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Bacteroidetes/química , Bacteroidetes/genética , Composição de Bases , DNA Bacteriano/genética , Lipídeos/análise , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Especificidade da Espécie
8.
Environ Pollut ; 255(Pt 2): 113327, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31600703

RESUMO

Fish-associated antibiotic resistance genes (ARGs) have attracted increasing attention due to their potential risks to human beings via the food chain. However, data are scarce regarding the antibiotic resistance in fish themselves. Herein, the antibiotic resistance genes (ARGs) were assessed in the gut of four major Chinese freshwater carp (i.e., silver carp, grass carp, bighead carp, and crucian carp) from food retail markets. Results show that the abundances of target ARGs (e.g., tetA, tetO, tetQ, tetW, sulI, sulII, and blaTEM-1) and class 1 integrase (intI1) were in the range 9.4 × 10-6 - 1.6 × 10-1 and 6.7 × 10-5 - 5.2 × 10-2 gene copies per 16S rRNA gene, respectively. The sulI, sulII, and tetQ strongly correlated with silver and mercury resistance genes (e.g., silE and merR). The microbial taxa of fish gut could be partly separated among retail markets based on the PCA analysis. About 15.0% of the OTUs in fish gut were shared and 74.5% of the shared OTUs were identified as Acidobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Firmicutes, and Proteobacteria. These phyla may constitute the core microbiota in the guts of the four Chinese freshwater carp. The possible ARG hosts were revealed based on the network analysis, and the presence of pathogen-associated resistant genera in fish gut highlights the need to fully understand their potential human health risks.


Assuntos
Carpas/microbiologia , Farmacorresistência Bacteriana/genética , Microbioma Gastrointestinal/efeitos dos fármacos , Alimentos Marinhos/microbiologia , Acidobacteria/efeitos dos fármacos , Acidobacteria/genética , Acidobacteria/isolamento & purificação , Animais , Antibacterianos/farmacologia , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Chloroflexi/efeitos dos fármacos , Chloroflexi/genética , Chloroflexi/isolamento & purificação , Cianobactérias/efeitos dos fármacos , Cianobactérias/genética , Cianobactérias/isolamento & purificação , Firmicutes/efeitos dos fármacos , Firmicutes/genética , Firmicutes/isolamento & purificação , Água Doce/microbiologia , Microbioma Gastrointestinal/genética , Genes Bacterianos/genética , Metais Pesados/toxicidade , Proteobactérias/efeitos dos fármacos , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
9.
Parasit Vectors ; 12(1): 504, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31665056

RESUMO

BACKGROUND: Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this study we examined the whole-body microbial composition of R. pallescens from three locations in Panama. METHODS: We collected 89 R. pallescens specimens using Noireau traps in Attalea butyracea palms. We then extracted total DNA from whole-bodies of specimens and amplified bacterial microbiota using 16S rRNA metabarcoding PCR. The 16S libraries were sequenced on an Illumina MiSeq and analyzed using QIIME2 software. RESULTS: We found Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes to be the most abundant bacterial phyla across all samples. Geographical location showed the largest difference in microbial composition with northern Veraguas Province having the most diversity and Panama Oeste Province localities being most similar to each other. Wolbachia was detected in high abundance (48-72%) at Panama Oeste area localities with a complete absence of detection in Veraguas Province. No significant differences in microbial composition were detected between triatomine age class, primary blood meal source, or T. cruzi infection status. CONCLUSIONS: We found biogeographical regions differ in microbial composition among R. pallescens populations in Panama. While overall the microbiota has bacterial taxa consistent with previous studies in triatomine microbial ecology, locality differences are an important observation for future studies. Geographical heterogeneity in microbiomes of vectors is an important consideration for future developments that leverage microbiomes for disease control.


Assuntos
Bactérias/classificação , Doença de Chagas/transmissão , Insetos Vetores/microbiologia , Microbiota , Rhodnius/microbiologia , Actinobacteria/classificação , Actinobacteria/genética , Análise de Variância , Animais , Bactérias/genética , Bacteroidetes/classificação , Bacteroidetes/genética , Biodiversidade , Código de Barras de DNA Taxonômico , Ecossistema , Firmicutes/classificação , Firmicutes/genética , Biblioteca Gênica , Humanos , Insetos Vetores/fisiologia , Panamá , Filogeografia , Reação em Cadeia da Polimerase , Proteobactérias/classificação , Proteobactérias/genética , RNA Ribossômico 16S/química , Rhodnius/fisiologia
10.
Curr Microbiol ; 76(12): 1525-1530, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31602501

RESUMO

A Gram-negative, aerobic, oval-shaped, and light red pigmented bacterium, designated T6-1T, was isolated from the mash of wine collected from a wine-making laboratory simulated fermenter located in Beijing, China. The optimal growth of T6-1T occurred at 30 °C, pH 7.0 with 1% NaCl. The sole respiratory quinone was menaquinone-7 (MK-7). The principal cellular fatty acids (>5%) were iso-C15:0, iso-C17:0 3OH, C16:1 ω5c, and iso-C17:0. The major polar lipids were PE (phosphatidylethanolamine), PL (unidentified phospholipid), and L1-2 (unidentified lipids). 16S rRNA phylogenetic analysis indicated that strain T6-1T belonged to the genus Pontibacter. The 16S rRNA gene sequence of strain T6-1T was most similar to Pontibacter amylolyticus 9-2T (95.92%). The genomic DNA G+C content of strain T6-1 was 50.34 mol%. The digital DNA-DNA relatedness and average nucleotide identity value between T6-1T and 9-2T was 20.20% and 74.18%, respectively. Polyphasic taxonomy analysis indicated that strain T6-1T represents a novel species of the genus Pontibacter, for which the name Pontibacter beigongshangensis sp. nov. is proposed, with the type strain T6-1T (= CGMCC 1.17104T = KCTC 72413T).


Assuntos
Bacteroidetes/classificação , Vinho/microbiologia , Bacteroidetes/química , Bacteroidetes/citologia , Bacteroidetes/genética , Composição de Bases , Reatores Biológicos/microbiologia , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Environ Sci Pollut Res Int ; 26(28): 29052-29064, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31392612

RESUMO

The quality assessment of water, supplied to the end user, is an essential part to assess the physical, chemical, and biological status of water, which impacts on human health. For the quality assessment of drinking water treatment plants and distribution systems of Hyderabad City and Mehran University of Engineering and Technology, Jamshoro, Pakistan, 13 surface drinking water samples were collected from three treatment plants, two of Hyderabad City, including WASA treatment plant and its distribution system (n = 5), Hala Nakka treatment plant and its distribution system (n = 6), and Mehran University Employees Cooperative Housing Society (MUECHS) treatment plant and its distribution system (n = 2). Physicochemical parameters of all drinking water samples were in the range compared to EPA and WHO guidelines, except in L-12 sample. Notably, no free-chlorine was detected in all samples. In metagenomics analysis, targeting V3-V4 hypervariable region of 16S rRNA gene, in QIIME2 environment, high bacterial prevalence was observed in all samples. On average, 348 OTUs were observed per sample. Among all samples, treated water sample from the Hala Nakka Treatment Plant (HNTR) was the most diverse sample in bacterial composition (Shannon 7.51 and Simpsons reciprocal indices 0.98). Overall, Proteobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Actinobacteria were the five most abundant phyla (relative abundances of 43.6, 37.9, 8.5, 2.5, and 2.4 percent, respectively). Notably, Cyanobacteria are well-known toxin producers which effect the human, and animal health. At genus level, Flavobacterium (4.86%) and Aquirestis (3.77%) were the most abundant genera. Functional predictions, based on 16S rRNA gene by PICRUSt, predicted 6909 KEGG orthologies, relating to 245 KEGG pathways. Among the predicted pathways of KEGG orthologies, pathways to human infections were also found. In conclusion, this study gave a deep insight into bacterial contamination in drinking water samples of Hyderabad City and MUECHS treatment plants and water quality status in Hyderabad and Mehran University of Engineering and Technology.


Assuntos
Água Potável/microbiologia , Monitoramento Ambiental , Metagenoma , Purificação da Água , Actinobacteria/genética , Bacteroidetes/genética , Cloro , Cidades , Cianobactérias/classificação , Habitação , Humanos , Metagenômica , Paquistão , Proteobactérias/genética , RNA Ribossômico 16S/genética , Universidades , Qualidade da Água
12.
Bioresour Technol ; 291: 121865, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31369926

RESUMO

Bacterial community structure and metabolic function during solid waste decomposition were investigated using Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states, respectively. Results showed that bacterial community diversity and structure differed in aerobic phase, anaerobic acid phase, and methanogenic phase. Anaerobic acid phase had significantly (p < 0.05) higher richness. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant representatives with significant (p < 0.05) difference between three phases. Total nitrogen of solid waste and pH of leachate were the important factors in shaping bacterial community composition. Bacterial metabolism, information storage and processing, and cellular processes and signaling were the primary functions during solid waste decomposition. Key function genes (amo, nar, nis, and nos) profiles suggested that nitrification and denitrifiation mainly occurred in AP and both AP and MP, respectively.


Assuntos
Microbiota , Filogenia , Resíduos Sólidos , Bacteroidetes/genética , Biodiversidade , Euryarchaeota/genética , Firmicutes/genética , Nitrificação , Nitrogênio/metabolismo , Proteobactérias/genética
13.
Sci Total Environ ; 686: 1104-1112, 2019 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-31412506

RESUMO

Identification of fecal contamination sources in surface water has become heavily dependent on quantitative PCR (qPCR) because this technique allows for the rapid enumeration of fecal indicator bacteria as well as the detection and quantification of fecal source-associated genetic markers in the environment. Identification of contamination sources in impaired waters is a prerequisite for developing best management practices to reduce future pollution. Proper management decisions rely on the quality and interpretation of qPCR data. In this study, we developed a method to determine analytical and process lower limits of detection (LLOD) and quantification (LLOQ) using two cattle-associated genetic markers targeting Bacteroidales. Analytical LLOD (ALLOD) for both CowM2 and CowM3 genetic markers in the qPCR assay were five gene copies per reaction. Using composite fecal DNA, the analytical LLOQ (ALLOQ) determined for CowM2 and CowM3 were 78 and 195 gene copies/reaction, respectively. When plasmid DNA was used, the ALLOQ for CowM2 and CowM3 were 46 and 20 gene copies/reaction, respectively. The process LLOD (PLLOD) for CowM2 and CowM3 were 0.4 and 0.02 mg feces/filter (wet weight), respectively. Using the standard deviation value of 0.25 as a cut-off point for LLOQ in regression analysis, the process LLOQ (PLLOQ) for CowM2 and CowM3 were 3.2 and 0.3 mg feces/filter, respectively. These results indicate that CowM3 exhibited superior performance characteristics compared with CowM2 for fecal samples collected from our geographical region. Moreover, the method for calculating LLOD and LLOQ developed here can be applied to other microbial source tracking studies.


Assuntos
Bacteroidetes/isolamento & purificação , Monitoramento Ambiental/métodos , Fezes/microbiologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Microbiologia da Água , Animais , Bactérias/isolamento & purificação , Bacteroidetes/química , Bacteroidetes/genética , Bovinos , Marcadores Genéticos , Limite de Detecção
14.
Int J Mol Sci ; 20(14)2019 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-31373310

RESUMO

Bacteria colonize most of the human body, and the female genital tract is not an exception. While the existence of a vaginal microbiota has been well established, the upper genital tract has been considered a sterile environment, with a general assumption that bacterial presence is associated with adverse clinical manifestation. However, recent metagenomic studies identified specific patterns of microbiota colonizing the uterus, fallopian tubes, ovaries, and placenta. These results need confirmation and further investigations since the data are only scarce. Bacterial colonization of these sites appears different from the vaginal one, despite evidence that vaginal bacteria could ascend to the upper genital tract through the cervix. Are these bacteria only commensal or do they play a role in the physiology of the female upper genital tract? Which are the genera that may have a negative and a positive impact on the female reproductive function? The aim of this review is to critically present all available data on upper genital tract microbiota and discuss its role in human reproduction, ranging from the technical aspects of these types of analyses to the description of specific bacterial genera. Although still very limited, research focusing on genital colonization of bacteria other than the vaginal milieu might bring novel insights into physiopathology of human reproduction.


Assuntos
Tubas Uterinas/microbiologia , Lactobacillus/isolamento & purificação , Ovário/microbiologia , Placenta/microbiologia , Útero/microbiologia , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Feminino , Humanos , Lactobacillus/genética , Microbiota/fisiologia , Gravidez , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
15.
Sci Total Environ ; 689: 1181-1191, 2019 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-31466158

RESUMO

Efforts to understand the environmental and biological factors that influence the dynamics of microbial communities have received substantial attention in microbial ecology. In this study, Illumina MiSeq high-throughput sequencing technology was used to examine the microbial community structure of activated sludge in municipal wastewater treatment systems (Chuzhou city, China). Overall, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were the most dominant phyla in the five activated sludge samples. However, the community structure of nitrifying bacteria was relatively simple, and diversity was low; only AOB (Nitrosomonas) and NOB (Nitrospira) were detected. The dominant bacteria in the anaerobic sludge, anoxic sludge and oxic sludge were the same, and each bacterial species was relatively uniform, with differences only in proportions. Redundancy analysis indicated that pH, TP and COD were strong environmental factors influencing the bacterial community distribution. PICRUSt was used to describe the metabolic and functional abilities of the activated sludge bacterial communities. The results emphasized the vast genetic diversity of these organisms, which are involved in various essential processes such as amino acid transport and metabolism, energy production and conversion, cell wall/membrane/envelope/biogenesis, signal transduction mechanisms, and carbohydrate transport and metabolism. Activated sludge of municipal wastewater treatment systems can be ranked in the following order based on the 16S rRNA gene copy numbers of the detected phylotypes: S1 > S2 > S4 > S5 > S3. This study provides basic data and a theoretical analysis of the optimal design and operation in wastewater treatment plants.


Assuntos
Microbiota , Eliminação de Resíduos Líquidos , Águas Residuárias/microbiologia , Bactérias/classificação , Bacteroidetes/genética , China , Firmicutes , Filogenia , Proteobactérias/genética , Esgotos/microbiologia
16.
J Microbiol ; 57(11): 967-975, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31463791

RESUMO

A polyphasic taxonomy approach was used to characterize strain YBJ-36T, isolated from a freshwater lake in Taiwan. Phylogenetic analyses, based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters), indicated that strain YBJ-36T formed a phylogenetic lineage in the genus Mucilaginibacter. 16S rRNA gene sequence similarity indicated that strain YBJ-36T is closely related to species within the genus Mucilaginibacter (93.8-97.8% sequence similarity) and is most similar to Mucilaginibacter fluminis TTM-2T (97.8%), followed by Mucilaginibacter roseus TTM-1T (97.2%). Microbiological analyses demonstrated that strain YBJ-36T is Gram-negative, aerobic, non-motile, rod-shaped, surrounded by a thick capsule, and forms pink-colored colonies. Strain YBJ-36T grew between 20-40°C (optimal range, 35-37°C), pH 5.5-7.0 (optimal pH of 6) and 0-2% NaCl (optimal concentration, 0.5%). The predominant fatty acids of strain YBJ-36T are iso-C15:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c), the major polar lipid is phosphatidylethanolamine, the major polyamine is homospermidine, and the major isoprenoid quinone is MK-7. The draft genome is approximately 4.63 Mb in size with a G+C content of 42.8 mol%. Strain YBJ-36T exhibited less than 35% DNA-DNA relatedness with Mucilaginibacter fluminis TTM-2T and Mucilaginibacter roseus TTM-1T. Based on phenotypic and genotypic properties and phylogenetic inference, strain YBJ-36T should be classified in a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter limnophilus sp. nov. is proposed. The type strain is YBJ-36T (= BCRC 81056T = KCTC 52811T = LMG 30058T).


Assuntos
Bacteroidetes/classificação , Bacteroidetes/isolamento & purificação , Lagos/microbiologia , Filogenia , Microbiologia da Água , Técnicas de Tipagem Bacteriana , Bacteroidetes/genética , Bacteroidetes/fisiologia , Composição de Bases , Benzoquinonas/química , DNA Bacteriano/genética , Ácidos Graxos/química , Lipídeos/química , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas/química , Poliaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan , Sequenciamento Completo do Genoma
17.
Nat Commun ; 10(1): 3460, 2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31371723

RESUMO

Bacteria often produce antimicrobial toxins to compete in microbial communities. Here we identify a family of broad-spectrum peptide toxins, named bacteroidetocins, produced by Bacteroidetes species. We study this toxin family using phenotypic, mutational, bioinformatic, and human metagenomic analyses. Bacteroidetocins are related to class IIa bacteriocins of Gram-positive bacteria and kill members of the Bacteroidetes phylum, including Bacteroides, Parabacteroides, and Prevotella gut species, as well as pathogenic Prevotella species. The bacteroidetocin biosynthesis genes are found in horizontally acquired mobile elements, which likely allow dissemination within the gut microbiota and may explain their wide distribution in human populations. Bacteroidetocins may have potential applications in microbiome engineering and as therapeutics for polymicrobial diseases such as bacterial vaginosis and periodontal disease.


Assuntos
Antibacterianos/biossíntese , Toxinas Bacterianas/biossíntese , Bacteriocinas/biossíntese , Bacteriocinas/genética , Bacteroidetes/metabolismo , Microbioma Gastrointestinal/fisiologia , Peptídeos/metabolismo , Antibacterianos/farmacologia , Proteínas de Bactérias/biossíntese , Proteínas de Bactérias/genética , Proteínas de Bactérias/farmacologia , Toxinas Bacterianas/genética , Toxinas Bacterianas/farmacologia , Bacteriocinas/farmacologia , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Sequência de Bases , Feminino , Microbioma Gastrointestinal/genética , Trato Gastrointestinal/microbiologia , Transferência Genética Horizontal/genética , Humanos , Sequências Repetitivas Dispersas , Metagenômica , Testes de Sensibilidade Microbiana , Peptídeos/genética , Peptídeos/farmacologia , Prevotella/efeitos dos fármacos , Análise de Sequência de Proteína , Vaginose Bacteriana
18.
Biomed Res Int ; 2019: 6361320, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31309109

RESUMO

Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.


Assuntos
Bacteroidetes/genética , Microbioma Gastrointestinal/genética , Metagenoma , Interações Microbianas/genética , Família Multigênica , Obesidade , Bacteroidetes/metabolismo , Humanos , Obesidade/genética , Obesidade/microbiologia
19.
Nat Microbiol ; 4(10): 1727-1736, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31285584

RESUMO

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.


Assuntos
Bacteriófagos/genética , Coevolução Biológica , Microbioma Gastrointestinal , Animais , Bacteriófagos/classificação , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/virologia , DNA Viral/genética , Fezes/virologia , Feminino , Variação Genética , Humanos , Masculino , Filogenia , Filogeografia , Primatas/virologia
20.
Arch Microbiol ; 201(10): 1385-1397, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31338542

RESUMO

Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90-96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrate-active against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes.


Assuntos
Bactérias/classificação , Bactérias/enzimologia , Búfalos , Bovinos , Dieta , Microbiota/fisiologia , Rúmen/microbiologia , Animais , Bactérias/genética , Bacteroidetes/genética , Búfalos/microbiologia , Bovinos/microbiologia , Celulases/metabolismo , Dieta/veterinária , Fibras na Dieta , Glicosídeo Hidrolases/metabolismo , Metagenoma , Metagenômica , Consórcios Microbianos/genética , Filogenia
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