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1.
PLoS One ; 15(5): e0232699, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32374760

RESUMO

The metal hyperaccumulator Azolla filiculoides is accompanied by a microbiome potentially supporting plant during exposition to heavy metals. We hypothesized that the microbiome exposition to selected heavy metals will reveal metal tolerant strains. We used Next Generation Sequencing technique to identify possible metal tolerant strains isolated from the metal-treated plant (Pb, Cd, Cr(VI), Ni, Au, Ag). The main dominants were Cyanobacteria and Proteobacteria constituting together more than 97% of all reads. Metal treatment led to changes in the composition of the microbiome and showed significantly higher richness in the Pb-, Cd- and Cr-treated plant in comparison with other (95-105 versus 36-44). In these treatments the share of subdominant Actinobacteria (0.4-0.8%), Firmicutes (0.5-0.9%) and Bacteroidetes (0.2-0.9%) were higher than in non-treated plant (respectively: 0.02, 0.2 and 0.001%) and Ni-, Au- and Ag-treatments (respectively: <0.4%, <0.2% and up to 0.2%). The exception was Au-treatment displaying the abundance 1.86% of Bacteroidetes. In addition, possible metal tolerant genera, namely: Acinetobacter, Asticcacaulis, Anabaena, Bacillus, Brevundimonas, Burkholderia, Dyella, Methyloversatilis, Rhizobium and Staphylococcus, which form the core microbiome, were recognized by combining their abundance in all samples with literature data. Additionally, the presence of known metal tolerant genera was confirmed: Mucilaginibacter, Pseudomonas, Mycobacterium, Corynebacterium, Stenotrophomonas, Clostridium, Micrococcus, Achromobacter, Geobacter, Flavobacterium, Arthrobacter and Delftia. We have evidenced that A. filiculoides possess a microbiome whose representatives belong to metal-resistant species which makes the fern the source of biotechnologically useful microorganisms for remediation processes.


Assuntos
Cádmio/farmacologia , Cromo/farmacologia , Gleiquênias/microbiologia , Chumbo/farmacologia , Microbiota/efeitos dos fármacos , Microbiota/genética , Poluentes do Solo/farmacologia , Actinobacteria/efeitos dos fármacos , Actinobacteria/genética , Actinobacteria/metabolismo , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/genética , Bacteroidetes/metabolismo , Biodegradação Ambiental , Cádmio/metabolismo , Cromo/metabolismo , DNA Bacteriano/genética , DNA Bacteriano/isolamento & purificação , Firmicutes/efeitos dos fármacos , Firmicutes/genética , Firmicutes/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Chumbo/metabolismo , RNA Ribossômico 16S/genética , Microbiologia do Solo
2.
NPJ Syst Biol Appl ; 6(1): 14, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415097

RESUMO

Cells can sense changes in their extracellular environment and subsequently adapt their biomass composition. Nutrient abundance defines the capability of the cell to produce biomass components. Under nutrient-limited conditions, resource allocation dramatically shifts to carbon-rich molecules. Here, we used dynamic biomass composition data to predict changes in growth and reaction flux distributions using the available genome-scale metabolic models of five eukaryotic organisms (three heterotrophs and two phototrophs). We identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion. Surprisingly, our calculations of model sensitivity and biosynthetic cost showed that free energy of biomass metabolites is the main driver of biosynthetic cost and not molecular weight, thus explaining the high costs of arginine and histidine. We demonstrated how metabolic models can accurately predict the complexity of interwoven mechanisms in response to stress over the course of growth.


Assuntos
Eucariotos/crescimento & desenvolvimento , Eucariotos/metabolismo , Nitrogênio/metabolismo , Animais , Bacteroidetes/metabolismo , Biomassa , Células CHO/metabolismo , Carbono/metabolismo , Isótopos de Carbono , Chlorella vulgaris/metabolismo , Cricetulus , Genoma , Saccharomyces cerevisiae/metabolismo , Inanição , Yarrowia/metabolismo
3.
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
4.
Sci Rep ; 10(1): 1876, 2020 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024862

RESUMO

Over the past 15 years, massive gas hydrate deposits have been studied extensively in Joetsu Basin, Japan Sea, where they are associated primarily with active gas chimney structures. Our research documents the discovery of spheroidal microdolomite aggregates found in association with other impurities inside of these massive gas hydrates. The microdolomites are often conjoined and show dark internal cores occasionally hosting saline fluid inclusions. Bacteroidetes sp. are concentrated on the inner rims of microdolomite grains, where they degrade complex petroleum-macromolecules present as an impurity within yellow methane hydrate. These oils show increasing biodegradation with depth which is consistent with the microbial activity of Bacteroidetes. Further investigation of these microdolomites and their contents can potentially yield insight into the dynamics and microbial ecology of other hydrate localities. If microdolomites are indeed found to be ubiquitous in both present and fossil hydrate settings, the materials preserved within may provide valuable insights into an unusual microhabitat which could have once fostered ancient life.


Assuntos
Organismos Aquáticos/metabolismo , Bacteroidetes/metabolismo , Carbonato de Cálcio/química , Sedimentos Geológicos/microbiologia , Magnésio/química , Metano/metabolismo , Organismos Aquáticos/química , Bacteroidetes/química , Biodegradação Ambiental , Fósseis , Sedimentos Geológicos/química , Microbiota , Petróleo/metabolismo , Água do Mar/química , Água do Mar/microbiologia
5.
Biotechnol Lett ; 42(3): 341-356, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31897850

RESUMO

Efforts to elucidate the relationships between microorganisms and metal corrosion were mainly directed to understanding the formation of biofilm structures grown on corroded surfaces. The emergence of high throughput DNA sequencing techniques has helped in the description of microbial species involved directly and indirectly in the corrosion processes of alloys. Coupled with sequencing from environmental samples, other methodologies such as metatranscriptome, metaproteomics and metabolomics have allowed a new horizon to be opened on the understanding of the role of corrosive microbial biofilm. Several groups of bacteria and archaea were identified, showing the dominance of Proteobacteria in several samples analyzed and members of groups that previously received less attention, such as Firmicutes and Bacteroidetes. Our research also shows that metagenomic studies describe the presence of various Archaea domain thermophilic and methanogenic groups associated with metal corrosion. Thus, opening the prospect of describing new microbial groups as possible participants in this current global concern.


Assuntos
Archaea/metabolismo , Bacteroidetes/metabolismo , Firmicutes/metabolismo , Metais/metabolismo , Proteobactérias/metabolismo , Corrosão
6.
Appl Microbiol Biotechnol ; 103(21-22): 9155-9168, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31641816

RESUMO

Wastewater treatment plants (WWTPs) rely mainly on the microbial assemblages to contribute significantly for the removal of organic pollutants and nutrients. However, limited information is available on the ecological driving forces underlying the turnover of prokaryotic communities across wastewater treatment processes (i.e., from influents (IFs) and effluents (EFs)) within WWTPs. Here, we used a combination of the 16S rRNA gene amplicon sequencing and a quantitative ecological null model analysis to explore the ecological processes governing the turnover of the prokaryotic communities and the dominant taxonomic taxa across wastewater treatment processes of five full-scale WWTPs in China. Our results indicated that a significant variation in the composition of prokaryotic communities and the dominant taxa between IFs and EFs. The analysis of the environmental sources of indicator OTUs showed that a relatively lower abundance of the sludge/sewage and human guts associated OTUs in EFs than in IFs. Ecological null models revealed that among the ecological processes, deterministic processes were dominant in controlling the turnover of the overall communities from IFs to EFs, whereas the relative importance of deterministic processes varied among the dominant taxa (i.e., Bacteroidetes > Proteobacteria > Gammaproteobacteria > Firmicutes > Betaproteobacteria). However, the assembly of IF and EF communities was influenced mainly by the deterministic and stochastic processes, respectively. In addition, our results indicated that EF communities have a higher phylogenetic diversity than those of the IF communities, but the abundance of prokaryotic 16S rRNA genes was lower in EFs than in IFs. Overall, our study provides a novel insight of the assembly mechanisms underlying the turnover of prokaryotic communities during wastewater treatment processes.


Assuntos
Bacteroidetes/classificação , Betaproteobacteria/classificação , Firmicutes/classificação , Gammaproteobacteria/classificação , Águas Residuárias/microbiologia , Purificação da Água/métodos , Bacteroidetes/genética , Bacteroidetes/metabolismo , Betaproteobacteria/genética , Betaproteobacteria/metabolismo , China , Firmicutes/genética , Firmicutes/metabolismo , Gammaproteobacteria/genética , Gammaproteobacteria/metabolismo , RNA Ribossômico 16S/genética , Águas Residuárias/química , Poluentes Químicos da Água/análise
7.
Environ Pollut ; 255(Pt 1): 113190, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31541828

RESUMO

Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.


Assuntos
Bacteroidetes/metabolismo , Óleos/análise , Petróleo/análise , Proteobactérias/metabolismo , Poluentes do Solo/análise , Solo/química , Bacteroidetes/classificação , Bacteroidetes/isolamento & purificação , Biodegradação Ambiental , Carbono/análise , Lubrificantes/análise , Nitrogênio/análise , Proteobactérias/classificação , Proteobactérias/isolamento & purificação , Microbiologia do Solo
8.
mBio ; 10(4)2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409684

RESUMO

Studies of the gut microbiota have dramatically increased in recent years as the importance of this microbial ecosystem to human health and disease is better appreciated. The Bacteroidales are the most abundant order of bacteria in the healthy human gut and induce both health-promoting and disease-promoting effects. There are more than 55 species of gut Bacteroidales with extensive intraspecies genetic diversity, especially in regions involved in the synthesis of molecules that interact with other bacteria, the host, and the diet. This property necessitates the study of diverse species and strains. In recent years, the genetic toolkit to study these bacteria has greatly expanded, but we still lack a facile system for creating deletion mutants and allelic replacements in diverse strains, especially with the rapid increase in resistance to the two antibiotics used for genetic manipulation. Here, we present a new versatile and highly efficient vector suite that allows the creation of allelic deletions and replacements in multiresistant strains of Bacteroides and Parabacteroides using a gain-of-function system based on polysaccharide utilization. These vectors also allow for easy counterselection independent of creating a mutant background strain, using a toxin from a type VI secretion system of Bacteroides fragilis Toxin production during counterselection is induced with one of two different molecules, providing flexibility based on strain phenotypes. This family of vectors greatly facilitates functional genetic analyses and extends the range of gut Bacteroidales strains that can be genetically modified to include multiresistant strains that are currently genetically intractable with existing genetic tools.IMPORTANCE We have entered an era when studies of the gut microbiota are transitioning from basic questions of composition and host effects to understanding the microbial molecules that underlie compositional shifts and mediate health and disease processes. The importance of the gut Bacteroidales to human health and disease and their potential as a source of engineered live biotherapeutics make these bacteria of particular interest for in-depth mechanistic study. However, there are still barriers to the genetic analysis of diverse Bacteroidales strains, limiting our ability to study important host and community phenotypes identified in these strains. Here, we have overcome many of these obstacles by constructing a series of vectors that allow easy genetic manipulation in diverse gut Bacteroides and Parabacteroides strains. These constructs fill a critical need and allow streamlined allelic replacement in diverse gut Bacteroidales, including the growing number of multiantibiotic-resistant strains present in the modern-day human intestine.


Assuntos
Bacteroidetes/genética , Microbioma Gastrointestinal , Engenharia Genética/métodos , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Toxinas Bacterianas/genética , Toxinas Bacterianas/metabolismo , Bacteroides/genética , Bacteroides/metabolismo , Bacteroidetes/metabolismo , Farmacorresistência Bacteriana Múltipla/genética , Marcadores Genéticos , Vetores Genéticos , Humanos , Inulina/genética , Inulina/metabolismo , Metaloendopeptidases/genética , Metaloendopeptidases/metabolismo , Mutação , Regiões Promotoras Genéticas , Ramnose/metabolismo
9.
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
10.
ISME J ; 13(11): 2800-2816, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31316134

RESUMO

We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010-2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.


Assuntos
Bacteroidetes/genética , Bacteroidetes/metabolismo , Diatomáceas/metabolismo , Polissacarídeos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Bacteroidetes/classificação , Diatomáceas/crescimento & desenvolvimento , Eutrofização , Genoma Bacteriano , Metagenoma , Mar do Norte
11.
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
12.
Environ Microbiol ; 21(11): 4002-4019, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31314938

RESUMO

This study determines the natural product biosynthesis and full coding potential within the bacterial genus Aquimarina. Using comprehensive phylogenomics and functional genomics, we reveal that phylogeny instead of isolation source [host-associated (HA) vs. free-living (FL) habitats] primarily shape the inferred metabolism of Aquimarina species. These can be coherently organized into three major functional clusters, each presenting distinct natural product biosynthesis profiles suggesting that evolutionary trajectories strongly underpin their secondary metabolite repertoire and presumed bioactivities. Aquimarina spp. are highly versatile bacteria equipped to colonize HA and FL microniches, eventually displaying opportunistic behaviour, owing to their shared ability to produce multiple glycoside hydrolases from diverse families. We furthermore uncover previously underestimated, and highly complex secondary metabolism for the genus by detecting 928 biosynthetic gene clusters (BGCs) across all genomes, grouped in 439 BGC families, with polyketide synthases (PKSs), terpene synthases and non-ribosomal peptide synthetases (NRPSs) ranking as the most frequent BGCs encoding drug-like candidates. We demonstrate that the recently described cuniculene (trans-AT PKS) BGC is conserved among, and specific to, the here delineated A. megaterium-macrocephali-atlantica phylogenomic clade. Our findings provide a timely and in-depth perspective of an under-explored yet emerging keystone taxon in the cycling of organic matter and secondary metabolite production in marine ecosystems.


Assuntos
Bacteroidetes/metabolismo , Flavobacteriaceae/metabolismo , Sedimentos Geológicos/microbiologia , Água do Mar/microbiologia , Metabolismo Secundário/genética , Organismos Aquáticos/classificação , Organismos Aquáticos/genética , Organismos Aquáticos/metabolismo , Bacteroidetes/classificação , Bacteroidetes/genética , Carbono/metabolismo , Ecossistema , Flavobacteriaceae/classificação , Flavobacteriaceae/genética , Genômica/métodos , Glicosídeo Hidrolases/genética , Família Multigênica , Peptídeo Sintases/genética , Filogenia , Policetídeo Sintases/genética
13.
PLoS One ; 14(6): e0218118, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31185060

RESUMO

We investigated whether supplementation with the barley line BARLEYmax (Tantangara; BM), which contains three fermentable fibers (fructan, ß-glucan, and resistant starch), modifies the microbiota in cecal and distal colonic digesta in addition to short-chain fatty acids (SCFAs) production more favorably than supplementation with a high-ß-glucan barley line (BG012; BG). Male Sprague-Dawley rats were randomly divided into 3 groups that were fed an AIN-93G-based diet that contained 5% fiber provided by cellulose (control), BM or BG. Four weeks after starting the respective diets, the animals were sacrificed and digesta from the cecum, proximal colon and distal colon were collected and the SCFA concentrations were quantified. Microbiota in the cecal and distal colonic digesta were analyzed by 16S rRNA sequencing. The concentrations of acetate and n-butyrate in cecal digesta were significantly higher in the BM and BG groups than in the control group, whereas the concentration of total SCFAs in cecal digesta was significantly higher only in the BM group than in the control group. The concentrations of acetate and total SCFAs in the distal colonic digesta were significantly higher only in the BM group than in the control group. The abundance of Bacteroidetes in cecal digesta was significantly higher in the BM group than in the control group. In contrast, the abundance of Firmicutes in cecal digesta was significantly lower in the BM and BG groups than in the control group. These results indicated that BM increased the concentration of total SCFAs in the distal colonic digesta. These changes might have been caused by fructan and resistant starch in addition to ß-glucan. In conclusion, fermentable fibers in BM reached the distal colon and modified the microbiota, leading to an increase in the concentration of total SCFAs in the distal colonic digesta, more effectively compared with the high-ß-glucan barley line (BG).


Assuntos
Bacteroidetes/metabolismo , Ceco/microbiologia , Colo/microbiologia , Ácidos Graxos/biossíntese , Hordeum , Microbiota/efeitos dos fármacos , beta-Glucanas/farmacologia , Ração Animal , Animais , Ratos , Ratos Sprague-Dawley
14.
Int J Biol Macromol ; 136: 547-558, 2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31201911

RESUMO

An exopolysaccharide producing strain AK103T was isolated from Sambharlake, Rajasthan, India. Based on polyphasic taxonomy, the strain AK103T was found to be a novel species for which the name Natronotalea sambharensis sp. nov. is proposed. The strain was able to secrete (1.2 gL-1) EPS under optimum conditions. The FT-IR spectroscopy revealed that EPS had carboxyl, hydroxyl, carbonyl and sulfate ester groups. The high performance liquid chromatography (HPLC), gel permeation chromatography (GPC) and NMR revealed that the exopolysaccharide was composed of mannose, glucose and glucuronic acid with a molecular weight of 4.6 × 106 KDa. This novel EPS was designated as Nat-103. Interestingly, the EPS was found to have antioxidant activity and in vitro antioxidant studies showed that DPPH (2,2-diphenyl-1-picrylhydrazyl) activity increased in a dose dependent manner. Furthermore, EPS Nat-103 was able to produce gold nanoparticles which were further characterized by FT-IR, DLS and Zeta potential (ZP).


Assuntos
Bacteroidetes/química , Polissacarídeos Bacterianos/química , Polissacarídeos Bacterianos/isolamento & purificação , Antioxidantes/química , Antioxidantes/isolamento & purificação , Antioxidantes/metabolismo , Bacteroidetes/metabolismo , Ouro/química , Cinética , Nanopartículas Metálicas/química , Peso Molecular , Monossacarídeos/análise , Filogenia , Polissacarídeos Bacterianos/biossíntese , Reologia , Ácidos Urônicos/análise
15.
PLoS One ; 14(5): e0216336, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31071110

RESUMO

A genome-scale metabolic network reconstruction of Salinibacter ruber DSM13855 is presented here. To our knowledge, this is the first metabolic model of an organism in the phylum Rhodothermaeota. This model, which will be called iMB631, was reconstructed based on genomic and biochemical data available on the strain Salinibacter ruber DSM13855. This network consists of 1459 reactions, 1363 metabolites and 631 genes. Model evaluation was performed based on existing biochemical data in the literature and also by performing laboratory experiments. For growth on different carbon sources, we show that iMB631 is able to correctly predict the growth in 91% of cases where growth has been observed experimentally and 83% of conditions in which S. ruber did not grow. The F-score was 93%, demonstrating a generally acceptable performance of the model. Based on the predicted flux distributions, we found that under certain autotrophic condition, a reductive tricarboxylic acid cycle (rTCA) has fluxes in all necessary reactions to support autotrophic growth. To include special metabolites of the bacterium, salinixanthin biosynthesis pathway was modeled based on the pathway proposed recently. For years, main glucose consumption pathway has been under debates in S. ruber. Using flux balance analysis, iMB631 predicts pentose phosphate pathway, rather than glycolysis, as the active glucose consumption method in the S. ruber.


Assuntos
Processos Autotróficos/fisiologia , Bacteroidetes , Redes Reguladoras de Genes/fisiologia , Genoma Bacteriano/fisiologia , Redes e Vias Metabólicas/fisiologia , Modelos Biológicos , Bacteroidetes/genética , Bacteroidetes/metabolismo
16.
Nutrients ; 11(5)2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31075850

RESUMO

4-Hydroxy-3-methoxycinnamic acid (HMCA), a hydroxycinnamic acid derivative, is abundant in fruits and vegetables, including oranges, carrots, rice bran, and coffee beans. Several beneficial effects of HMCA have been reported, including improvement of metabolic abnormalities in animal models and human studies. However, its mitigating effects on high-fat diet (HFD)-induced obesity, and the mechanism underlying these effects, remain to be elucidated. In this study, we demonstrated that dietary HMCA was efficacious against HFD-induced weight gain and hepatic steatosis, and that it improved insulin sensitivity. These metabolic benefits of HMCA were ascribable to 3-(4-hydroxy-3-methoxyphenyl)propionic acid (HMPA) produced by gut microbiota. Moreover, conversion of HMCA into HMPA was attributable to a wide variety of microbes belonging to the phylum Bacteroidetes. We further showed that HMPA modulated gut microbes associated with host metabolic homeostasis by increasing the abundance of organisms belonging to the phylum Bacteroidetes and reducing the abundance of the phylum Firmicutes. Collectively, these results suggest that HMPA derived from HMCA is metabolically beneficial, and regulates hepatic lipid metabolism, insulin sensitivity, and the gut microbial community. Our results provide insights for the development of functional foods and preventive medicines, based on the microbiota of the intestinal environment, for the prevention of metabolic disorders.


Assuntos
Ácidos Cumáricos/farmacologia , Dieta , Microbioma Gastrointestinal/efeitos dos fármacos , Metabolismo dos Lipídeos/efeitos dos fármacos , Fígado/efeitos dos fármacos , Obesidade/metabolismo , Propionatos/farmacologia , Animais , Bacteroidetes/efeitos dos fármacos , Bacteroidetes/crescimento & desenvolvimento , Bacteroidetes/metabolismo , Citrus sinensis/química , Coffea/química , Ácidos Cumáricos/metabolismo , Daucus carota/química , Dieta Hiperlipídica/efeitos adversos , Fígado Gorduroso/etiologia , Fígado Gorduroso/prevenção & controle , Firmicutes/crescimento & desenvolvimento , Firmicutes/metabolismo , Trato Gastrointestinal/metabolismo , Trato Gastrointestinal/microbiologia , Resistência à Insulina , Fígado/metabolismo , Fígado/patologia , Masculino , Doenças Metabólicas/etiologia , Doenças Metabólicas/metabolismo , Doenças Metabólicas/patologia , Doenças Metabólicas/prevenção & controle , Camundongos Endogâmicos C57BL , Camundongos Obesos , Obesidade/complicações , Obesidade/etiologia , Oryza/química , Plantas Comestíveis/química , Propionatos/metabolismo , Ganho de Peso/efeitos dos fármacos
17.
Nat Commun ; 10(1): 2043, 2019 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-31053724

RESUMO

Unlike proteins, glycan chains are not directly encoded by DNA, but by the specificity of the enzymes that assemble them. Theoretical calculations have proposed an astronomical number of possible isomers (> 1012 hexasaccharides) but the actual diversity of glycan structures in nature is not known. Bacteria of the Bacteroidetes phylum are considered primary degraders of polysaccharides and they are found in all ecosystems investigated. In Bacteroidetes genomes, carbohydrate-degrading enzymes (CAZymes) are arranged in gene clusters termed polysaccharide utilization loci (PULs). The depolymerization of a given complex glycan by Bacteroidetes PULs requires bespoke enzymes; conversely, the enzyme composition in PULs can provide information on the structure of the targeted glycans. Here we group the 13,537 PULs encoded by 964 Bacteroidetes genomes according to their CAZyme composition. We find that collectively Bacteroidetes have elaborated a few thousand enzyme combinations for glycan breakdown, suggesting a global estimate of diversity of glycan structures much smaller than the theoretical one.


Assuntos
Proteínas de Bactérias/genética , Bacteroidetes/genética , Enzimas/genética , Genoma Bacteriano/genética , Polissacarídeos/metabolismo , Proteínas de Bactérias/metabolismo , Bacteroidetes/metabolismo , Enzimas/metabolismo , Loci Gênicos , Isomerismo , Polissacarídeos/química
18.
Bioresour Technol ; 281: 202-208, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30822641

RESUMO

In the present study, ectopic fermentation systems were treated with both solid and liquid waste from livestock. Then, the various physicochemical properties and compositions of microbial communities in different waste straws treatments were compared. The addition of thermophilic bacteria was beneficial to the decomposition of litter, and it improved the fermentation process. Proteobacteria, Bacteroidetes, and Firmicutes were the predominant types in the fermentation vessels, and the presence of the phyla Proteobacteria and Bacteroidetes was correlated with factors prevailing in the mature phase. Furthermore, pig manure with sawdust, rape stem, and rice chaff and pig manure with sawdust, rice straw, and rice chaff vessels had higher concentrations of dissolved nitrogen, which were conducive to the conversion of fermentation wastes into useful fertilizer. These results demonstrate the feasibility of using rape stem and rice straw as padding materials during the treatment of both liquid and solid livestock waste in ectopic fermentation systems.


Assuntos
Fermentação , Esterco/microbiologia , Microbiota , Aerobiose , Animais , Bacteroidetes/metabolismo , Firmicutes/metabolismo , Proteobactérias/metabolismo , Suínos
19.
Environ Pollut ; 248: 506-515, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30831347

RESUMO

The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ±â€¯68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ±â€¯118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 109 copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.


Assuntos
Actinobacteria/metabolismo , Alphaproteobacteria/metabolismo , Anaerobiose/fisiologia , Bacteroidetes/metabolismo , Biodegradação Ambiental , Dibenzofuranos Policlorados/análise , Dioxinas/análise , Poluentes do Solo/análise , Poluição Ambiental/análise , Microbiota/fisiologia , Oxirredução , Oxigênio/metabolismo , RNA Ribossômico 16S , Solo , Microbiologia do Solo
20.
Microbiome ; 7(1): 48, 2019 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-30914068

RESUMO

BACKGROUND: The piglets' transition from milk to solid feed induces a succession of bacterial communities, enhancing the hosts' ability to harvest energy from dietary carbohydrates. To reconstruct microbial carbohydrate metabolism in weanling pigs, this study combined 16S rRNA gene sequencing (n = 191) and shotgun metagenomics (n = 72). RESULTS: Time and wheat content in feed explained most of the variation of the microbiota as assessed by 16S rRNA gene sequencing in weanling pigs. De novo metagenomic binning reconstructed 360 high-quality genomes that represented 11 prokaryotic and 1 archaeal phylum. Analysis of carbohydrate metabolism in these genomes revealed that starch fermentation is carried out by a consortium of Firmicutes expressing extracellular α-(1 → 4)-glucan branching enzyme (GH13) and Bacteroidetes expressing periplasmic neopullulanase (GH13) and α-glucosidase (GH97). Fructans were degraded by extracellular GH32 enzymes from Bacteriodetes and Lactobacillus. Lactose fermentation by ß-galactosidases (GH2 and GH42) was identified in Firmicutes. In conclusion, the assembly of 360 high-quality genomes as the first metagenomic reference for swine intestinal microbiota allowed identification of key microbial contributors to degradation of starch, fructans, and lactose. CONCLUSIONS: Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. Our study thus enables improvement of feeding models with higher feed efficiency and better pathogen control for weanling pigs.


Assuntos
Bactérias/classificação , Carboidratos da Dieta/metabolismo , Metagenômica/métodos , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Bacteroidetes/metabolismo , DNA Bacteriano/genética , DNA Ribossômico/genética , Firmicutes/genética , Firmicutes/isolamento & purificação , Firmicutes/metabolismo , Microbioma Gastrointestinal , Lactobacillus/genética , Lactobacillus/isolamento & purificação , Lactobacillus/metabolismo , Masculino , Filogenia , Suínos
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