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1.
Microbiol Res ; 236: 126436, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32179388

RESUMO

Trichoderma longibrachiatum EF5 is an endophytic fungal antagonist of rice. It is used for the control of soil-borne fungal pathogens-Sclerotium rolfsii and Macrophomina phaseolina. We demonstrate that T. longibrachiatum EF5 inhibits the growth of these pathogens on direct interaction as well as via the production of the microbial volatile organic compounds (mVOCs). The mVOCs reduced mycelial growth and inhibited the production of sclerotia by altering the mycelial structure. We profiled 138 mVOCs, when T. longibrachiatum EF5 interacted with the two pathogens. During these interactions, several compounds are up- or downregulated by T. longibrachiatum EF5, including longifolene, caryophyllene,1-Butanol 2-methyl, cedrene, and cuprenene. These compounds are involved in the biosynthetic pathways of the sesquiterpenoid and alkane, and the degradation pathway of trimethylamine. We provide an insight into the multiple modes by which T. longibrachiatum EF5 exerts antagonistic actions, such as hyperparasitism, competitions, and antibiosis via mVOCs. In contrast to their antimicrobial properties, these metabolites could also promote plant growth.


Assuntos
Agaricales/efeitos dos fármacos , Antibiose , Ascomicetos/efeitos dos fármacos , Trichoderma/metabolismo , Compostos Orgânicos Voláteis/farmacologia , Agaricales/crescimento & desenvolvimento , Ascomicetos/crescimento & desenvolvimento , Agentes de Controle Biológico , Interações Microbianas , Doenças das Plantas/microbiologia , Microbiologia do Solo , Compostos Orgânicos Voláteis/química
2.
Nat Commun ; 11(1): 754, 2020 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-32029713

RESUMO

A major unresolved question is how bacteria living in complex communities respond to environmental changes. In communities, biotic interactions may either facilitate or constrain evolution depending on whether the interactions expand or contract the range of ecological opportunities. A fundamental challenge is to understand how the surrounding biotic community modifies evolutionary trajectories as species adapt to novel environmental conditions. Here we show that community context can dramatically alter evolutionary dynamics using a novel approach that 'cages' individual focal strains within complex communities. We find that evolution of focal bacterial strains depends on properties both of the focal strain and of the surrounding community. In particular, there is a stronger evolutionary response in low-diversity communities, and when the focal species have a larger genome and are initially poorly adapted. We see how community context affects resource usage and detect genetic changes involved in carbon metabolism and inter-specific interaction. The findings demonstrate that adaptation to new environmental conditions should be investigated in the context of interspecific interactions.


Assuntos
Microbiota/fisiologia , Adaptação Fisiológica , Fenômenos Fisiológicos Bacterianos , Biodiversidade , Evolução Biológica , Inglaterra , Variação Genética , Genoma Bacteriano , Interações Microbianas/genética , Interações Microbianas/fisiologia , Microbiota/genética , Chuva/microbiologia , Microbiologia da Água
3.
PLoS One ; 15(1): e0228108, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32004342

RESUMO

Although organic matter may accumulate sometimes (e.g. lignocellulose in peat bog), most natural biodegradation processes are completed until full mineralization. Such transformations are often achieved by the concerted action of communities of interacting microbes, involving different species each performing specific tasks. These interactions can give rise to novel "community-intrinsic" properties, through e.g. activation of so-called "silent genetic pathways" or synergistic interplay between microbial activities and functions. Here we studied the microbial community-based degradation of keratin, a recalcitrant biological material, by four soil isolates, which have previously been shown to display synergistic interactions during biofilm formation; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. We observed enhanced keratin weight loss in cultures with X. retroflexus, both in dual and four-species co-cultures, as compared to expected keratin degradation by X. retroflexus alone. Additional community intrinsic properties included accelerated keratin degradation rates and increased biofilm formation on keratin particles. Comparison of secretome profiles of X. retroflexus mono-cultures to co-cultures revealed that certain proteases (e.g. serine protease S08) were significantly more abundant in mono-cultures, whereas co-cultures had an increased abundance of proteins related to maintaining the redox environment, e.g. glutathione peroxidase. Hence, one of the mechanisms related to the community intrinsic properties, leading to enhanced degradation from co-cultures, might be related to a switch from sulfitolytic to proteolytic functions between mono- and co-cultures, respectively.


Assuntos
Bactérias/metabolismo , Queratinas/metabolismo , Consórcios Microbianos/fisiologia , Biodegradação Ambiental , Biofilmes , Técnicas de Cocultura , Interações Microbianas , Microbiologia do Solo
4.
Nature ; 578(7796): 588-592, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32076271

RESUMO

Elucidating elementary mechanisms that underlie bacterial diversity is central to ecology1,2 and microbiome research3. Bacteria are known to coexist by metabolic specialization4, cooperation5 and cyclic warfare6-8. Many species are also motile9, which is studied in terms of mechanism10,11, benefit12,13, strategy14,15, evolution16,17 and ecology18,19. Indeed, bacteria often compete for nutrient patches that become available periodically or by random disturbances2,20,21. However, the role of bacterial motility in coexistence remains unexplored experimentally. Here we show that-for mixed bacterial populations that colonize nutrient patches-either population outcompetes the other when low in relative abundance. This inversion of the competitive hierarchy is caused by active segregation and spatial exclusion within the patch: a small fast-moving population can outcompete a large fast-growing population by impeding its migration into the patch, while a small fast-growing population can outcompete a large fast-moving population by expelling it from the initial contact area. The resulting spatial segregation is lost for weak growth-migration trade-offs and a lack of virgin space, but is robust to population ratio, density and chemotactic ability, and is observed in both laboratory and wild strains. These findings show that motility differences and their trade-offs with growth are sufficient to promote diversity, and suggest previously undescribed roles for motility in niche formation and collective expulsion-containment strategies beyond individual search and survival.


Assuntos
Escherichia coli/fisiologia , Interações Microbianas , Movimento , Biodiversidade , Escherichia coli/citologia , Escherichia coli/crescimento & desenvolvimento , Escherichia coli/isolamento & purificação , Fezes/microbiologia , Flagelos/fisiologia , Modelos Biológicos , Análise Espacial
5.
Int J Food Microbiol ; 317: 108498, 2020 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-31918247

RESUMO

Aspergillus carbonarius consistently produces large amounts of ochratoxin A (OTA), a mycotoxin with nephrotoxic effects on animals and humans. In the present study, we analyzed the transcriptional changes associated to OTA production in three atypical non-ochratoxigenic strains of A. carbonarius. In addition, in vitro interactions between ochratoxigenic strains of A. carbonarius and A. niger and non-ochratoxigenic strains of A. carbonarius and A. tubingensis were studied in order to evaluate their potential for controlling OTA production. RNA-seq analysis revealed that there are 696 differentially expressed genes identified in the three non-OTA-producing strains, including 280 up-regulated and 333 down-regulated genes. A functional and gene ontology enrichment analysis revealed that the processes related to metabolic and oxidation processes, associated with functions such as oxidoreductase and hydrolase activity were down regulated. All the genes related with OTA biosynthesis in A. carbonarius were the most down-regulated genes in non-ochratoxigenic strains. We also showed that these strains possess a deleterious mutation in the AcOTApks gene required for OTA biosynthesis. Moreover, one of these strains gave the best control of OTA production resulting in an OTA reduction of 98-100% in co-inoculation with an ochratoxigenic strain of A. niger and an OTA reduction of 79-89% with an ochratoxigenic strain of A. carbonarius. Results of this study provided novel insights into the knowledge of the OTA biosynthetic pathway in these non-ochratoxigenic wild strains, and showed the biocontrol potential of these strains.


Assuntos
Aspergillus/genética , Aspergillus/metabolismo , Agentes de Controle Biológico/metabolismo , Interações Microbianas/fisiologia , Aspergillus/classificação , Perfilação da Expressão Gênica , Humanos , Hidrolases/metabolismo , Ocratoxinas/biossíntese , Oxirredutases/metabolismo , Vitis/microbiologia
6.
J Med Microbiol ; 69(2): 147-161, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31961787

RESUMO

During infections, bacterial pathogens can engage in a variety of interactions with each other, ranging from the cooperative sharing of resources to deadly warfare. This is especially relevant in opportunistic infections, where different strains and species often co-infect the same patient and interact in the host. Here, we review the relevance of these social interactions during opportunistic infections using the human pathogen Pseudomonas aeruginosa as a case example. In particular, we discuss different types of pathogen-pathogen interactions, involving both cooperation and competition, and elaborate on how they impact virulence in multi-strain and multi-species infections. We then review evolutionary dynamics within pathogen populations during chronic infections. We particuarly discuss how local adaptation through niche separation, evolutionary successions and antagonistic co-evolution between pathogens can alter virulence and the damage inflicted on the host. Finally, we outline how studying bacterial social dynamics could be used to manage infections. We show that a deeper appreciation of bacterial evolution and ecology in the clinical context is important for understanding microbial infections and can inspire novel treatment strategies.


Assuntos
Interações Microbianas , Infecções Oportunistas/microbiologia , Infecções por Pseudomonas/microbiologia , Pseudomonas aeruginosa/fisiologia , Animais , Coinfecção/microbiologia , Humanos , Pseudomonas aeruginosa/genética
7.
Nat Commun ; 11(1): 285, 2020 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-31941905

RESUMO

Predator-prey interactions play important roles in the cycling of marine organic matter. Here we show that a Gram-negative bacterium isolated from marine sediments (Pseudoalteromonas sp. strain CF6-2) can kill Gram-positive bacteria of diverse peptidoglycan (PG) chemotypes by secreting the metalloprotease pseudoalterin. Secretion of the enzyme requires a Type II secretion system. Pseudoalterin binds to the glycan strands of Gram positive bacterial PG and degrades the PG peptide chains, leading to cell death. The released nutrients, including PG-derived D-amino acids, can then be utilized by strain CF6-2 for growth. Pseudoalterin synthesis is induced by PG degradation products such as glycine and glycine-rich oligopeptides. Genes encoding putative pseudoalterin-like proteins are found in many other marine bacteria. This study reveals a new microbial interaction in the ocean.


Assuntos
Proteínas de Bactérias/metabolismo , Sedimentos Geológicos/microbiologia , Bactérias Gram-Positivas/fisiologia , Interações Microbianas/fisiologia , Pseudoalteromonas/fisiologia , Alanina/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Cristalografia por Raios X , Ácido Glutâmico/metabolismo , Metaloproteases/química , Metaloproteases/genética , Metaloproteases/metabolismo , Simulação de Acoplamento Molecular , Mutação , Peptidoglicano/metabolismo , Água do Mar/microbiologia , Staphylococcus/fisiologia , Sistemas de Secreção Tipo II/metabolismo
8.
Biol Cell ; 112(3): 92-101, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31922615

RESUMO

BACKGROUND: Non-typhoidal Salmonella (NTS) causes a severe invasive syndrome (iNTS disease) described in HIV-positive adults. The impact of HIV-1 on Salmonella pathogenesis and the molecular basis for the differences between these bacteria and classical diarrhoeal S. Typhimurium remains unclear. RESULTS: Here, we show that iNTS-associated S. Typhimurium Sequence Type 313 (ST313) bacteria show greater intracellular survival in primary human macrophages, compared with a 'classical' diarrhoeal S. Typhimurium ST19 isolate. The increased intracellular survival phenotype of ST313 is more pronounced in HIV-infected macrophages. We explored the possibility that the bacteria take advantage of the HIV-associated viral-containing compartments created in human macrophages that have low pH. Confocal fluorescence microscopy and focussed ion beam-scanning electron microscopy tomography showed that Salmonella did not co-localise extensively with HIV-positive compartments. CONCLUSION: The capacity of ST313 bacteria to survive better than ST19 bacteria within primary human macrophages is enhanced in cells pre-infected with HIV-1. Our results indicate that the ST313 bacteria do not directly benefit from the niche created by the virus in HIV-1-infected macrophages, and that they might take advantage from a more globally modified host cell. SIGNIFICANCE: A better understanding of the interplay between HIV-1 and Salmonella is important not only for these bacteria but also for other opportunistic pathogens.


Assuntos
Interações entre Hospedeiro e Microrganismos/fisiologia , Interações Microbianas , Salmonella typhimurium/crescimento & desenvolvimento , Coinfecção/microbiologia , Citoplasma/microbiologia , Citoplasma/virologia , Tomografia com Microscopia Eletrônica/métodos , Infecções por HIV/complicações , HIV-1/crescimento & desenvolvimento , Humanos , Macrófagos/microbiologia , Macrófagos/fisiologia , Macrófagos/virologia , Interações Microbianas/fisiologia , Microscopia Confocal , Cultura Primária de Células , Infecções por Salmonella/etiologia
9.
Nat Commun ; 11(1): 309, 2020 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-31949154

RESUMO

Cellular interactions are a major driver for the assembly and functioning of microbial communities. Their strengths are shown to be highly variable in nature; however, it is unclear how such variations regulate community behaviors. Here we construct synthetic Lactococcus lactis consortia and mathematical models to elucidate the role of interaction variability in ecosystem succession and to further determine if casting variability into modeling empowers bottom-up predictions. For a consortium of bacteriocin-mediated cooperation and competition, we find increasing the variations of cooperation, from either altered labor partition or random sampling, drives the community into distinct structures. When the cooperation and competition are additionally modulated by pH, ecosystem succession becomes jointly controlled by the variations of both interactions and yields more diversified dynamics. Mathematical models incorporating variability successfully capture all of these experimental observations. Our study demonstrates interaction variability as a key regulator of community dynamics, providing insights into bottom-up predictions of microbial ecosystems.


Assuntos
Ecossistema , Consórcios Microbianos/fisiologia , Interações Microbianas/fisiologia , Biologia Sintética , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Técnicas de Cocultura , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos/genética , Concentração de Íons de Hidrogênio , Lactococcus lactis/genética , Lactococcus lactis/fisiologia , Consórcios Microbianos/genética , Interações Microbianas/genética , Modelos Teóricos
10.
Nat Commun ; 11(1): 362, 2020 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-31953381

RESUMO

The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug-microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.


Assuntos
Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/metabolismo , Microbioma Gastrointestinal/efeitos dos fármacos , Microbioma Gastrointestinal/fisiologia , Metagenômica , Adulto , Antibacterianos/farmacologia , Antidepressivos/farmacologia , Índice de Massa Corporal , Estudos de Casos e Controles , Estudos de Coortes , Biologia Computacional , Ecossistema , Fezes/microbiologia , Feminino , Humanos , Síndrome do Intestino Irritável/tratamento farmacológico , Síndrome do Intestino Irritável/microbiologia , Laxantes/farmacologia , Masculino , Metformina/farmacologia , Interações Microbianas/efeitos dos fármacos , Pessoa de Meia-Idade , Inibidores da Bomba de Prótons/farmacologia
11.
Ann Clin Microbiol Antimicrob ; 19(1): 5, 2020 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-31992328

RESUMO

Recurrent vulvovaginal infections (RVVI) has not only become an epidemiological and clinical problem but also include large social and psychological consequences. Understanding the mechanisms of both commensalism and pathogenesis are necessary for the development of efficient diagnosis and treatment strategies for these enigmatic vaginal infections. Through this review, an attempt has been made to analyze vaginal microbiota (VMB) from scratch and to provide an update on its current understanding in relation to health and common RVVI i.e. bacterial vaginosis, vulvovaginal candidiaisis and Trichomoniasis, making the present review first of its kind. For this, potentially relevant studies were retrieved from data sources and critical analysis of the literature was made. Though, culture-independent methods have greatly unfolded the mystery regarding vaginal bacterial microbiome, there are only a few studies regarding the composition and diversity of vaginal mycobiome and different Trichomonas vaginalis strains. This scenario suggests a need of further studies based on comparative genomics of RVVI pathogens to improve our perceptive of RVVI pathogenesis that is still not clear (Fig. 5). Besides this, the review details the rationale for Lactobacilli dominance and changes that occur in healthy VMB throughout a women's life. Moreover, the list of possible agents continues to expand and new species recognised in both health and VVI are updated in this review. The review concludes with the controversies challenging the widely accepted dogma i.e. "VMB dominated with Lactobacilli is healthier than a diverse VMB". These controversies, over the past decade, have complicated the definition of vaginal health and vaginal infections with no definite conclusion. Thus, further studies on newly recognised microbial agents may reveal answers to these controversies. Conversely, VMB of women could be an answer but it is not enough to just look at the microbiology. We have to look at the woman itself, as VMB which is fine for one woman may be troublesome for others. These differences in women's response to the same VMB may be determined by a permutation of behavioural, cultural, genetic and various other anonymous factors, exploration of which may lead to proper definition of vaginal health and disease.


Assuntos
Candidíase Vulvovaginal , Microbiota , Vaginite por Trichomonas , Vagina/microbiologia , Vaginose Bacteriana , Biofilmes/crescimento & desenvolvimento , Candida/isolamento & purificação , Candida/metabolismo , Candida albicans/isolamento & purificação , Candida albicans/metabolismo , Candidíase Vulvovaginal/microbiologia , Candidíase Vulvovaginal/patologia , Candidíase Vulvovaginal/transmissão , Coinfecção/microbiologia , Coinfecção/parasitologia , Feminino , Gardnerella vaginalis/isolamento & purificação , Interações entre Hospedeiro e Microrganismos , Humanos , Lactobacillus/isolamento & purificação , Lactobacillus/metabolismo , Interações Microbianas , Microbiota/fisiologia , Recidiva , Vaginite por Trichomonas/parasitologia , Vaginite por Trichomonas/patologia , Vaginite por Trichomonas/transmissão , Trichomonas vaginalis/isolamento & purificação , Trichomonas vaginalis/metabolismo , Vagina/parasitologia , Vaginose Bacteriana/microbiologia , Vaginose Bacteriana/patologia , Vaginose Bacteriana/transmissão , Fatores de Virulência/metabolismo
12.
Plant Dis ; 104(1): 121-128, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31730414

RESUMO

Aureobasidium pullulans is used as a biocontrol agent for fire blight protection in organic apple and pear production. We assessed colonization of pome flowers by A. pullulans in orchards located near Corvallis, OR and Wenatchee, WA. Blossom Protect, a mix of A. pullulans strains CF10 and CF40, and its citrate-based companion, Buffer Protect, were sprayed at 70% bloom. Later in bloom, the population size of putative A. pullulans on flowers was estimated by dilution plating; plate scrapings of putative A. pullulans were then sampled and subjected to a PCR analysis. Sequenced PCR amplicons of the internal transcribed spacer region and the elongase gene confirmed the presence of A. pullulans, whereas a multiplex PCR with primers specific to CF10 and CF40 was used to determine the presence of the introduced strains. At Corvallis, a wet spring environment, A. pullulans, was recovered from most (>90%) Bartlett pear and Golden Delicious apple flowers sampled from experimental trees, regardless of whether the trees were treated with Blossom Protect. Nevertheless, population size estimates of A. pullulans on the flowers were correlated with the number of times Blossom Protect was sprayed on the trees. At Wenatchee, an arid spring environment, A. pullulans was detected on most flowers from trees treated with Blossom Protect, but only on a minority of flowers from nontreated controls. In both locations, the combined incidence of strains CF10 and CF40 on flowers averaged 89% on Blossom Protect-treated trees, but only 27% on adjacent, nontreated trees. During subsequent trials, the efficacy of Blossom Protect for fire blight control was compared with alternative yeast isolates, with each applied with Buffer Protect; local isolates of A. pullulans and Cryptococcus neoformans and a postharvest biocontrol strain of Cystofilobasidium infirmominiatum were used All yeast strains suppressed fire blight to a degree; however, in each of four trials, the level of suppression was highest with Blossom Protect, and it was significantly superior (P ≤ 0.05) to other yeast isolates in two of the trials. Because A. pullulans strains CF10 and CF40 were detected primarily on flowers on trees treated with Blossom Protect, and because they were detected much less frequently on nearby nontreated tress, we recommend treating every tree row with Blossom Protect at least once for organic fire blight suppression.


Assuntos
Ascomicetos , Frutas , Malus , Pyrus , Ascomicetos/genética , Ascomicetos/crescimento & desenvolvimento , DNA Fúngico/genética , Frutas/microbiologia , Malus/microbiologia , Interações Microbianas , Doenças das Plantas/microbiologia , Reação em Cadeia da Polimerase , Pyrus/microbiologia
13.
Bioresour Technol ; 296: 122317, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31677401

RESUMO

Effects of ferroferric oxide (Fe3O4) and organic carbon on co-metabolism of sulfate and organic carbon were investigated. With Fe3O4, the degradation of acetate and sulfate was inhibited when fed with acetate, while the degradation of acetate and propionate produced from ethanol was promoted when fed with ethanol. The dominant sulfate reducing bacteria (SRB) of acetate-fed reactors were Desulfobacteraceae (complete oxidizing SRB, CO-SRB) and Desulfurmonas (incomplete oxidizing SRB, IO-SRB). IO-SRBs of Desulfobulbus and Desulfomicrobium were dominant in ethanol-fed reactors. CO-SRB had higher competitiveness than methanogens to utilize acetate, while IO-SRBs might cooperate with methanogens to produce methane when dosed with ethanol and Fe3O4. The dosage of Fe3O4 changed the dominant methanogen from Methanosarcina to Methanosaeta with acetate as the organic carbon, while increased the relative abundance of Methanosaeta with ethanol as the organic carbon.


Assuntos
Carbono , Sulfatos , Metano , Interações Microbianas , Óxidos , Óxidos de Enxofre
14.
PLoS Comput Biol ; 15(12): e1007524, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31856158

RESUMO

The human gut microbiome is a complex ecosystem, in which hundreds of microbial species and metabolites coexist, in part due to an extensive network of cross-feeding interactions. However, both the large-scale trophic organization of this ecosystem, and its effects on the underlying metabolic flow, remain unexplored. Here, using a simplified model, we provide quantitative support for a multi-level trophic organization of the human gut microbiome, where microbes consume and secrete metabolites in multiple iterative steps. Using a manually-curated set of metabolic interactions between microbes, our model suggests about four trophic levels, each characterized by a high level-to-level metabolic transfer of byproducts. It also quantitatively predicts the typical metabolic environment of the gut (fecal metabolome) in approximate agreement with the real data. To understand the consequences of this trophic organization, we quantify the metabolic flow and biomass distribution, and explore patterns of microbial and metabolic diversity in different levels. The hierarchical trophic organization suggested by our model can help mechanistically establish causal links between the abundances of microbes and metabolites in the human gut.


Assuntos
Microbioma Gastrointestinal/fisiologia , Modelos Biológicos , Biomassa , Biologia Computacional , Simulação por Computador , Ecossistema , Humanos , Metaboloma , Interações Microbianas , Biologia de Sistemas
15.
BMC Genomics ; 20(1): 1022, 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31881845

RESUMO

BACKGROUND: In 2017, World Health Organization (WHO) published a catalogue of 12 families of antibiotic-resistant "priority pathogens" that are posing the greatest threats to human health. Six of these dreaded pathogens are known to infect the human gastrointestinal system. In addition to causing gastrointestinal and systemic infections, these pathogens can also affect the composition of other microbes constituting the healthy gut microbiome. Such aberrations in gut microbiome can significantly affect human physiology and immunity. Identifying the virulence mechanisms of these enteric pathogens are likely to help in developing newer therapeutic strategies to counter them. RESULTS: Using our previously published in silico approach, we have evaluated (and compared) Host-Pathogen Protein-Protein Interaction (HPI) profiles of four groups of enteric pathogens, namely, different species of Escherichia, Shigella, Salmonella and Vibrio. Results indicate that in spite of genus/ species specific variations, most enteric pathogens possess a common repertoire of HPIs. This core set of HPIs are probably responsible for the survival of these pathogen in the harsh nutrient-limiting environment within the gut. Certain genus/ species specific HPIs were also observed. CONSLUSIONS: The identified bacterial proteins involved in the core set of HPIs are expected to be helpful in understanding the pathogenesis of these dreaded gut pathogens in greater detail. Possible role of genus/ species specific variations in the HPI profiles in the virulence of these pathogens are also discussed. The obtained results are likely to provide an opportunity for development of novel therapeutic strategies against the most dreaded gut pathogens.


Assuntos
Fenômenos Fisiológicos Bacterianos , Microbioma Gastrointestinal , Interações Hospedeiro-Patógeno , Infecções Bacterianas/metabolismo , Infecções Bacterianas/microbiologia , Proteínas de Bactérias , Biologia Computacional/métodos , Humanos , Interações Microbianas , Modelos Biológicos , Ligação Proteica , Mapeamento de Interação de Proteínas/métodos , Mapas de Interação de Proteínas
16.
BMC Genomics ; 20(Suppl 11): 945, 2019 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-31856723

RESUMO

BACKGROUND: Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment. For example, variants in gut microbiomes have been reported to be associated with several chronic conditions, such as inflammatory disease and irritable bowel syndrome. However, how microbial bacteria contribute to pathogenesis still remains unclear and major research questions in this domain remain unanswered. METHODS: We propose a split graph model to represent the composition and interactions of a given microbiome. We used metagenomes from Korean populations in this study. The dataset consists of three different types of samples, viz. mucosal tissue and stool from Crohn's disease patients and stool from healthy individuals. We use the split graph model to analyze the impact of microbial compositions on various host phenotypes. Utilizing the graph model, we have developed a pipeline that integrates genomic information and pathway analysis to characterize both critical informative components of inter-bacterial correlations and associations between bacterial taxa and various metabolic pathways. RESULTS: The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn's disease. We show that there are significant positive associations between detected taxonomic biomarkers as well as multiple functional modules in the split graph of mucosal tissue samples from CD patients. Bacteria Moraxellaceae and Pseudomonadaceae were detected as taxonomic biomarkers in CD groups. Higher abundance of these bacteria have been reported in previous study and several metabolic pathways associated with these bacteria were characterized in CD samples. CONCLUSIONS: The proposed pipeline provides a new way to approach the analysis of complex microbiomes. The results obtained from this study show great potential in unraveling mechansims in complex biological systems to understand how various components in such complex environments are associated with critical biological functions.


Assuntos
Biologia Computacional/métodos , Interações Microbianas/fisiologia , Microbiota , Modelos Biológicos , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biomarcadores , Doença de Crohn/metabolismo , Doença de Crohn/microbiologia , Microbioma Gastrointestinal/genética , Humanos , Redes e Vias Metabólicas , Metagenoma , Fenótipo
17.
PLoS One ; 14(12): e0227228, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31887213

RESUMO

Trichoderma has been used as an alternative to synthetic pesticides to control a variety of phytopathogenic fungi, oomycetes, and nematodes. Although its mechanism of pathogen suppression has been extensively studied, how Trichoderma interacts with non-target microbes is not well understood. Here, we investigated how two Trichoderma biological control agents (BCAs) interact with rhizosphere bacteria isolated from a tomato plant via secreted proteins, metabolites, and volatile compounds (VCs). Culture filtrates (CFs) of T. virens and T. harzianum, containing secreted proteins and metabolites, strongly inhibited (>75% reduction in growth) 39 and 19, respectively, out of 47 bacterial strains tested. Their CFs inhibited the remaining strains at lower degrees. Both metabolites and proteins are involved in inhibiting bacteria, but they seem to antagonize each other in inhibiting some strains. Trichoderma and bacteria suppressed the growth of each other using VCs. The secretion of antibacterial and antifungal molecules by T. virens and T. harzianum was significantly affected by VCs from some bacteria, suggesting that both Trichoderma BCAs and rhizosphere bacteria use VCs to influence each other in multiple ways. In light of these results, we discuss how metabolite-mediated interactions can potentially affect the effectiveness of biocontrol.


Assuntos
Bactérias/metabolismo , Agentes de Controle Biológico/metabolismo , Interações Microbianas , Rizosfera , Trichoderma/metabolismo , Bactérias/isolamento & purificação , Lycopersicon esculentum/microbiologia , Doenças das Plantas/microbiologia , Doenças das Plantas/prevenção & controle , Raízes de Plantas/microbiologia , Microbiologia do Solo , Compostos Orgânicos Voláteis/metabolismo
18.
J Microbiol ; 57(12): 1086-1094, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31680218

RESUMO

One of the advantages for initial survival of inhaled fungal spores in the respiratory tract is the ability for iron acquisition via hemolytic factor-production. To examine the ability of indoor Aspergillus and Penicillium affecting hemolysis, the secreted factors during the growth of thirteen strains from eight species were characterized in vitro for their hemolytic activity (HA) and CAMP-like reaction. The hemolytic index of HA on human blood agar of Aspergillus micronesiensis, Aspergillus wentii, Aspergillus westerdijkiae, Penicillium citrinum, Penicillium copticola, Penicillium paxilli, Penicillium steckii, and Penicillium sumatrense were 1.72 ± 0.34, 1.61 ± 0.41, 1.69 ± 0.16, 1.58 ± 0.46, 3.10 ± 0.51, 1.22 ± 0.19, 2.55 ± 0.22, and 1.90 ± 0.14, respectively. The secreted factors of an Aspergillus wentii showed high HA when grown in undernourished broth at 25°C at an exponential phase and were heat sensitive. Its secreted proteins have an estimated relative molecular weight over 50 kDa. Whereas, the factors of Penicillium steckii were secreted in a similar condition at a late exponential phase but showed low HA and heat tolerance. In a CAMP-like test with sheep blood, the synergistic hemolytic reactions between most tested mold strains and Staphylococcus aureus were identified. Moreover, the enhancement of α-hemolysis of Staphylococcus aureus could occur through the interaction of Staphylococcus aureus-sphingomyelinase and CAMP-like factors secreted from Aspergillus micronesiensis. Further studies on the characterization of purified hemolytic- and CAMP-like-factors secreted from Aspergillus wentii and Aspergillus micronesiensis may lead to more understanding of their involvement of hemolysis and cytolysis for fungal survival prior to pathogenesis.


Assuntos
Aspergillus/fisiologia , Hemólise , Interações Microbianas/fisiologia , Penicillium/fisiologia , Esfingomielina Fosfodiesterase/isolamento & purificação , Microbiologia do Ar , Animais , Aspergillus/isolamento & purificação , Toxinas Bacterianas , Sangue , Proteínas Hemolisinas , Temperatura Alta , Humanos , Técnicas In Vitro , Penicillium/isolamento & purificação , Ovinos , Esfingomielina Fosfodiesterase/metabolismo , Infecções Estafilocócicas , Staphylococcus aureus , Tailândia
19.
World J Microbiol Biotechnol ; 35(12): 182, 2019 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-31728757

RESUMO

Endophytes improve the host performance in areas of high plant endemicity. Paullinia cupana is an Amazonia plant species of economic and social importance due to the high caffeine concentration in its seeds. An interesting strategy to identify endophytic microorganisms with potential biotechnological application is to understand the factors that influence the endophytic community to rationalize the host management programs. We used the next-generation sequencing for bacterial 16S rRNA gene to examine how the P. cupana organ, genotype, and geographic location influenced its endophytic bacterial community. We obtained 1520 operational taxonomic units (OTUs) distributed in 19 phyla, 32 classes, 79 orders, 114 families and 174 genera. The P. cupana roots and leaves were specifically colonized by the bacterial genera Acidothermus and Porphyromonas, respectively, with high relative frequency. The plant organ type influenced the endophytic community's richness, diversity, OTUs composition, relative abundance of phyla and genera, and genera interaction network. However, the host plant genotype and geographic location influenced the composition and interaction among genera in the network analysis. Prevotella is a super-generalist genus in the interaction network of endophytic bacteria of P. cupana. This study revealed endophytic bacterial groups of importance to P. cupana and stressed that the host plant organ modulates the structure and interactions within this community. Our results indicated that the microbial community adapted to colonize P. cupana by adjusting to its composition and interaction network. The isolation of abundant and super-generalist bacterial genera shall help to examine their functionality to the composition and fitness of the endophytic community of P. cupana.


Assuntos
Bactérias/classificação , Bactérias/isolamento & purificação , Ecologia , Endófitos/classificação , Endófitos/isolamento & purificação , Paullinia/microbiologia , Bactérias/genética , Brasil , DNA Bacteriano/isolamento & purificação , Endófitos/genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Interações Microbianas , Microbiota/genética , Filogenia , Folhas de Planta/microbiologia , Raízes de Plantas/microbiologia , RNA Ribossômico 16S/genética , Sementes/microbiologia
20.
Int J Food Microbiol ; 311: 108350, 2019 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-31614280

RESUMO

Solid-state fermentation is a dynamic process involved with complex microbiome. Microbial structure and succession significantly affect the yield and quality of fermentation productions. Although the importance of microbial structure was extensively studied, the significance of microbial succession rate remains unclear in solid-state fermentation. To address this gap, we designed an in situ experiment in a typical distillery to characterize the effects of microbial succession rate. In this study, we found the process of strong-aroma Baijiu making could be divided into two stages according to fermentation parameters (starch, moisture, acidity, reducing sugar, alcohol, temperature). The early stage showed significantly (p < 0.05) higher microbial diversity than that of the later stage according to Shannon index. Compared with single cereal fermentation, mixed cereals fermentation showed slower microbial succession rate of stage shift. We found that Lactobacillus could reflect microbial succession rate of stage shift in strong-aroma Baijiu fermentation. Meanwhile, we found fermentation parameters could affect microbial succession rate of stage shift. Microbial diversity was significantly (p < 0.05) correlated with fermentation parameters. Moreover, molecular ecological network analysis (MENA) showed that succession rate of microbial community could affect microbial interactions. In addition, fermentation of mix cereals (sorghum, wheat, corn, rice and glutinous rice) increased the enrichment of Clostridiales from pit mud according to results of source tracking. Collectively, succession rate of microbial community could be an important trait to explain differences of microbial diversity and flavor profile from the perspective of microbial decline and enrichment. Our study highlighted the importance of microbial succession rate during strong-aroma Baijiu making process and provided a dynamic perspective to observe solid-state fermentation.


Assuntos
Clostridiales/metabolismo , Grão Comestível/microbiologia , Aromatizantes/metabolismo , Lactobacillus/metabolismo , Microbiota/fisiologia , Fermentação , Interações Microbianas , Odorantes , Paladar
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