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1.
Sci Total Environ ; 773: 145697, 2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-33940764

RESUMO

Microplastic (MP) pollution has attracted global attention due to the extensive use of plastic products. The hydrophobic MP surface provides a habitat for multiple microorganisms. Although there have been several studies on the impact of plastic particles on microbial communities, there are few reviews that have systematically summarized the interaction between MPs and microbes and their effects on human health and biochemical circulation. The discussions in this review will take place under the following topics: (1) MPs prompt colonization, biofilm generation, and transfer of environmental microbes; (2) the microbial communities can cause the morphological alterations and biodegradation of MPs; (3) MP-microbe combinations can induce the alteration of intestinal flora and hazard animal health; (4) the biogeochemical cycles affected by MP-microbe interactions. This review will highlight the close interactions between MPs and microorganisms, and provide suggestions for future studies.


Assuntos
Microbiota , Microplásticos , Animais , Biofilmes , Humanos , Interações Microbianas , Plásticos
2.
Bioresour Technol ; 331: 125029, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33831728

RESUMO

Numerous studies have revealed the effect of temperature and hydraulic retention time (HRT) on microbiota in sludge biological hydrolysis (BH). However, few scholars have explored the combined effect of these two critical BH parameters. This study explored the BH performance and community structures over 12 combined temperatures-HRT conditions for temperatures from 35 °C to 55 °C and HRTs from 1.5 days to 6.0 days. Results showed that the 12 combined conditions formed only six distinct community structures with each of them relating to a distinctive range of volatile suspended solid reduction rates. The nonmetric multidimensional scaling and species-species association analysis on the DNA sequencing data revealed that the community structure was greatly driven by the microbial interactions (e.g., heterogeneous commensalism and competition) under the effect of temperature and HRT. This study established the linkages among the combined BH temperature-HRT conditions, microbial interaction, microbial community, and BH performance.


Assuntos
Reatores Biológicos , Esgotos , Hidrólise , Interações Microbianas , Temperatura , Eliminação de Resíduos Líquidos
3.
Nat Med ; 27(4): 688-699, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33820995

RESUMO

Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion ( https://integrative-microbiomics.ntu.edu.sg ). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.


Assuntos
Bronquiectasia/microbiologia , Microbiota , Bronquiectasia/virologia , Progressão da Doença , Humanos , Metagenômica , Interações Microbianas/genética , Microbiota/genética , Filogenia
4.
Can J Microbiol ; 67(4): 301-309, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33703923

RESUMO

The aims of this study were to evaluate the ability of Campylobacter jejuni isolated from a poultry slaughterhouse to form biofilm in the presence and absence of Pseudomonas aeruginosa, and the effect of surface (stainless steel, polystyrene), temperature (7, 25, and 42 °C), and oxygen concentration (microaerophilic and aerobic conditions) on the formation of biofilm. The genes ahpC, cadF, clpP, dnaJ, docA, flaA, flaB, katA, kpsM, luxS, racR, and sodB, related to biofilm formation by C. jejuni, were also investigated. All isolates formed biofilm on stainless steel and on polystyrene, in both aerobic and microaerophilic atmospheres, including temperatures not optimal for C. jejuni growth (7 and 25 °C), and biofilm also was formed in the presence of P. aeruginosa. In dual-species biofilm on stainless steel, biofilm formation was 2-6 log CFU·cm-2 higher at 7 °C for all isolates, in comparison with monospecies biofilm. Ten genes (ahpC, cadF, clpP, dnaJ, docA, flaA, flaB, luxS, racR, and sodB) were detected in all isolates, but katA and kpsM were found in four and six isolates, respectively. The results obtained are of concern because the poultry C. jejuni isolates form biofilm in different conditions, which is enhanced in the presence of other biofilm formers, such as P. aeruginosa.


Assuntos
Biofilmes/crescimento & desenvolvimento , Campylobacter jejuni/fisiologia , Aves Domésticas/microbiologia , Pseudomonas aeruginosa/fisiologia , Matadouros , Animais , Campylobacter jejuni/isolamento & purificação , Interações Microbianas , Oxigênio/análise , Propriedades de Superfície , Temperatura
5.
Nat Commun ; 12(1): 1977, 2021 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-33785746

RESUMO

The scope of bioengineering is expanding from the creation of single strains to the design of microbial communities, allowing for division-of-labour, specialised sub-populations and interaction with "wild" microbiomes. However, in the absence of stabilising interactions, competition between microbes inevitably leads to the removal of less fit community members over time. Here, we leverage amensalism and competitive exclusion to stabilise a two-strain community by engineering a strain of Escherichia coli which secretes a toxin in response to competition. We show experimentally and mathematically that such a system can produce stable populations with a composition that is tunable by easily controllable parameters. This system creates a tunable, stable two-strain consortia while only requiring the engineering of a single strain.


Assuntos
Bioengenharia/métodos , Escherichia coli/fisiologia , Consórcios Microbianos/fisiologia , Interações Microbianas/fisiologia , Microbiota/fisiologia , Bacteriocinas/metabolismo , Escherichia coli/metabolismo , Modelos Biológicos
6.
Sci Rep ; 11(1): 6433, 2021 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-33742096

RESUMO

In response to the ongoing global pandemic, characterizing the molecular-level host interactions of the new coronavirus SARS-CoV-2 responsible for COVID-19 has been at the center of unprecedented scientific focus. However, when the virus enters the body it also interacts with the micro-organisms already inhabiting the host. Understanding the virus-host-microbiome interactions can yield additional insights into the biological processes perturbed by viral invasion. Alterations in the gut microbiome species and metabolites have been noted during respiratory viral infections, possibly impacting the lungs via gut-lung microbiome crosstalk. To better characterize microbial functions in the lower respiratory tract during COVID-19 infection, we carry out a functional analysis of previously published metatranscriptome sequencing data of bronchoalveolar lavage fluid from eight COVID-19 cases, twenty-five community-acquired pneumonia patients, and twenty healthy controls. The functional profiles resulting from comparing the sequences against annotated microbial protein domains clearly separate the cohorts. By examining the associated metabolic pathways, distinguishing functional signatures in COVID-19 respiratory tract microbiomes are identified, including decreased potential for lipid metabolism and glycan biosynthesis and metabolism pathways, and increased potential for carbohydrate metabolism pathways. The results include overlap between previous studies on COVID-19 microbiomes, including decrease in the glycosaminoglycan degradation pathway and increase in carbohydrate metabolism. The results also suggest novel connections to consider, possibly specific to the lower respiratory tract microbiome, calling for further research on microbial functions and host-microbiome interactions during SARS-CoV-2 infection.


Assuntos
/microbiologia , Interações Microbianas , Microbiota , Sistema Respiratório/microbiologia , /fisiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Humanos , Pulmão/microbiologia
7.
Nat Commun ; 12(1): 1498, 2021 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-33686084

RESUMO

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissect the microbial interactions in sugarcane ethanol fermentation by combinatorically reconstituting every possible combination of species, comprising approximately 80% of the biodiversity in terms of relative abundance. Functional landscape analysis shows that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we find that Lactobacillus amylovorus improves the yeast growth rate and ethanol yield by cross-feeding acetaldehyde, as shown by flux balance analysis and laboratory experiments. Our results suggest that Lactobacillus amylovorus could be considered a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment.


Assuntos
Fenômenos Fisiológicos Bacterianos , Etanol/metabolismo , Fermentação , Interações Microbianas/fisiologia , Saccharomyces cerevisiae/fisiologia , Acetaldeído/metabolismo , Acetaldeído/farmacologia , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Biodiversidade , Microbiologia Industrial/métodos , Lactobacillus/metabolismo , Microbiota , Melaço , Saccharomyces cerevisiae/efeitos dos fármacos , Saccharum
8.
Curr Opin Biotechnol ; 67: 149-157, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33561703

RESUMO

Multi-species microbial communities are ubiquitous in nature. The widespread prevalence of these communities is due to highly elaborated interactions among their members thereby accomplishing metabolic functions that are unattainable by individual members alone. Harnessing these communal capabilities is an emerging field in biotechnology. The rational intervention of microbial communities for the purpose of improved function has been facilitated in part by developments in multi-omics approaches, synthetic biology, and computational methods. Recent studies have demonstrated the benefits of rational interventions to human and animal health as well as agricultural productivity. Emergent technologies, such as in situ modification of complex microbial community and community metabolic modeling, represent an avenue to engineer sustainable microbial communities. In this opinion, we review relevant computational and experimental approaches to study and engineer microbial communities and discuss their potential for biotechnological applications.


Assuntos
Consórcios Microbianos , Microbiota , Animais , Biotecnologia , Humanos , Interações Microbianas , Biologia Sintética
9.
Environ Sci Technol ; 55(5): 3270-3282, 2021 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-33566597

RESUMO

Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.


Assuntos
Microbiota , Poluentes Químicos da Água , Antibacterianos , Biodegradação Ambiental , Interações Microbianas , Esgotos , Sulfametoxazol
10.
Microbiology (Reading) ; 167(3)2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33529149

RESUMO

The sixth Young Microbiologists Symposium on 'Microbe Signalling, Organisation and Pathogenesis' was scheduled to be held at the University of Southampton, UK, in late August 2020. However, due to the health and safety guidelines and travel restrictions as a response to the COVID-19 pandemic, the symposium was transitioned to a virtual format, a change embraced enthusiastically as the meeting attracted over 200 microbiologists from 40 countries. The event allowed junior scientists to present their work to a broad audience and was supported by the European Molecular Biology Organization, the Federation of European Microbiological Societies, the Society of Applied Microbiology, the Biochemical Society, the Microbiology Society and the National Biofilms Innovation Centre. Sessions covered recent advances in all areas of microbiology including: Secretion and transport across membranes, Gene regulation and signalling, Host-microbe interactions, and Microbial communities and biofilm formation. This report focuses on several of the highlights and exciting developments communicated during the talks and poster presentations.


Assuntos
Interações Hospedeiro-Patógeno , Interações Microbianas , Microbiologia/tendências , Biofilmes , Congressos como Assunto , Humanos , Reino Unido , Comunicação por Videoconferência
11.
Sci Total Environ ; 772: 145465, 2021 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-33571767

RESUMO

Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.


Assuntos
Fontes Termais , Biodiversidade , China , Temperatura Alta , Interações Microbianas , Filogenia , RNA Ribossômico 16S/genética , Temperatura
12.
Curr Opin Biotechnol ; 67: 72-79, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33517194

RESUMO

In nature, microorganisms live in multi-species communities allowing microbial interactions. These interactions are lost upon establishing a pure culture, increasing the metabolic burden and limiting the metabolic potential of the isolated microbe. In the past years, synthetic microbial co-cultivation, using well-defined consortia of two or more microbes, was increasingly explored for innovative applications in biotechnology. As such, interspecies interactions take place without the complexity of an open mixed culture, minimizing undesired side reactions. Ultimately, synthetic co-cultivation allows to take well-characterized microbes 'off-the-shelf' to create ecosystems with improved process capabilities. This review highlights some of the recent developments on co-cultivation, focusing on waste-to-chemicals conversions. It also addresses fundamental knowledge on microbial interactions deriving from these studies, which is important to further develop our ability to engineer functional co-cultures for bioproduction.


Assuntos
Ecossistema , Consórcios Microbianos , Biotecnologia , Técnicas de Cocultura , Interações Microbianas
14.
Nat Microbiol ; 6(2): 196-208, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33398099

RESUMO

Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures or synthetic assemblies. Here, we show how kefir, a natural milk-fermenting community of prokaryotes (predominantly lactic and acetic acid bacteria) and yeasts (family Saccharomycetaceae), realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microorganisms) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open the niche for the followers by making available metabolites such as amino acids and lactate. Through metabolomics, transcriptomics and large-scale mapping of inter-species interactions, we show how microorganisms poorly suited for milk survive in-and even dominate-the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.


Assuntos
Bactérias/metabolismo , Kefir/microbiologia , Interações Microbianas , Microbiota/fisiologia , Saccharomycetales/metabolismo , Ácido Acético/metabolismo , Bactérias/classificação , Bactérias/genética , Fermentação , Ácido Láctico/metabolismo , Metabolômica , Microbiota/genética , Filogenia , Saccharomycetales/classificação , Saccharomycetales/genética
15.
Planta ; 253(2): 25, 2021 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-33404767

RESUMO

MAIN CONCLUSION: The presence of Bacillus cereus plays a key role in clubroot suppression and improves plant biomass in pak choi. B. cereus is reported for the first time as a novel biocontrol agent against clubroot. Plasmodiophora brassicae Woronin causes a devastating infectious disease known as clubroot that is damaging to cruciferous vegetables. This study aimed to isolate beneficial bacteria from the rhizosphere soil of pak choi (Brassica campestris sp. chinensis) and to evaluate the ability of the isolate to reduce the severity of clubroot. Strains obtained from the rhizosphere of symptomless pak choi were first selected on the basis of their germination inhibition rate and effects on the viability of P. brassicae resting spores. Eight bacterial isolates had inhibitory effects against the resting spores of clubroot causing pathogen. However, MZ-12 showed the highest inhibitory effect at 73.4%. Inoculation with MZ-12 enhanced the plant biomass relative to plants grown without MZ-12 as well as P. brassicae infected plants. Furthermore, enhanced antioxidant enzymatic activities were observed in clubroot-infected plants during bacterial association. Co-inoculation of the plant with both P. brassicae and MZ-12 resulted in a 64% reduction of gall formation in comparison to plants inoculated with P. brassicae only. Three applications of MZ-12 to plants infected with P. brassicae at 7, 14 and 21 days after seeding (DAS) were more effective than one application and repressed root hair infection. According to 16S rDNA sequence analysis, strain MZ-12 was identified as had a 100% sequence similarity with type strain Bacillus cereus. The findings of the present study will facilitate further investigation into biological mechanisms of cruciferous clubroot control.


Assuntos
Bacillus cereus , Brassica , Doenças das Plantas , Raízes de Plantas , Plasmodioforídeos , Bacillus cereus/fisiologia , Brassica/microbiologia , Brassica/parasitologia , Interações Microbianas , Doenças das Plantas/microbiologia , Doenças das Plantas/parasitologia , Doenças das Plantas/prevenção & controle , Raízes de Plantas/microbiologia , Raízes de Plantas/parasitologia , Tumores de Planta/microbiologia , Tumores de Planta/parasitologia , Plasmodioforídeos/fisiologia
16.
Nat Methods ; 18(1): 37-39, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33398187
17.
Viruses ; 13(1)2021 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-33451106

RESUMO

Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a multifactorial disease in which dietary, genetic, immunological, and microbial factors are at play. The role of enteric viruses in IBD remains only partially explored. To date, epidemiological studies have not fully described the role of enteric viruses in inflammatory flare-ups, especially that of human noroviruses and rotaviruses, which are the main causative agents of viral gastroenteritis. Genome-wide association studies have demonstrated the association between IBD, polymorphisms of the FUT2 and FUT3 genes (which drive the synthesis of histo-blood group antigens), and ligands for norovirus and rotavirus in the intestine. The role of autophagy in defensin-deficient Paneth cells and the perturbations of cytokine secretion in T-helper 1 and T-helper 17 inflammatory pathways following enteric virus infections have been demonstrated as well. Enteric virus interactions with commensal bacteria could play a significant role in the modulation of enteric virus infections in IBD. Based on the currently incomplete knowledge of the complex phenomena underlying IBD pathogenesis, future studies using multi-sampling and data integration combined with new techniques such as human intestinal enteroids could help to decipher the role of enteric viruses in IBD.


Assuntos
Suscetibilidade a Doenças , Infecções por Enterovirus/complicações , Infecções por Enterovirus/virologia , Enterovirus/fisiologia , Interações Hospedeiro-Patógeno , Doenças Inflamatórias Intestinais/etiologia , Animais , Autofagia , Biomarcadores , Antígenos de Grupos Sanguíneos/genética , Antígenos de Grupos Sanguíneos/imunologia , Gerenciamento Clínico , Infecções por Enterovirus/epidemiologia , Microbioma Gastrointestinal , Humanos , Doenças Inflamatórias Intestinais/diagnóstico , Doenças Inflamatórias Intestinais/epidemiologia , Doenças Inflamatórias Intestinais/terapia , Interações Microbianas , Transdução de Sinais
18.
Viruses ; 13(1)2021 Jan 19.
Artigo em Inglês | MEDLINE | ID: mdl-33478119

RESUMO

Respiratory viral infections constitute a global public health concern. Among prevalent respiratory viruses, two pneumoviruses can be life-threatening in high-risk populations. In young children, they constitute the first cause of hospitalization due to severe lower respiratory tract diseases. A better understanding of their pathogenesis is still needed as there are no approved efficient anti-viral nor vaccine against pneumoviruses. We studied Respiratory Syncytial virus (RSV) and human Metapneumovirus (HMPV) in single and dual infections in three-dimensional cultures, a highly relevant model to study viral respiratory infections of the airway epithelium. Our investigation showed that HMPV is less pathogenic than RSV in this model. Compared to RSV, HMPV replicated less efficiently, induced a lower immune response, did not block cilia beating, and was more sensitive to IFNs. In dual infections, RSV-infected epithelia were less permissive to HMPV. By neutralizing IFNs in co-infection assays, we partially prevented HMPV inhibition by RSV and significantly increased the number of co-infected cells in the tissue. This suggests that interference in dual infection would be at least partly mediated by the host immune response. In summary, this work provides new insight regarding virus-host and virus-virus interactions of pneumoviruses in the airway epithelium. This could be helpful for the proper handling of at-risk patients.


Assuntos
Técnicas de Cultura de Células , Coinfecção , Interações Hospedeiro-Patógeno , Metapneumovirus/fisiologia , Interações Microbianas , Vírus Sincicial Respiratório Humano/fisiologia , Replicação Viral , Linhagem Celular , Humanos , Interferon Tipo I/farmacologia , Interferons/farmacologia , Metapneumovirus/efeitos dos fármacos , Infecções por Paramyxoviridae/virologia , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/efeitos dos fármacos , Esferoides Celulares
19.
Nat Commun ; 12(1): 672, 2021 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-33510148

RESUMO

Microbial species rarely exist in isolation. In naturally occurring microbial systems there is strong evidence for a positive relationship between species diversity and productivity of communities. The pervasiveness of these communities in nature highlights possible advantages for genetically engineered strains to exist in cocultures as well. Building synthetic microbial communities allows us to create distributed systems that mitigate issues often found in engineering a monoculture, especially as functional complexity increases. Here, we demonstrate a methodology for designing robust synthetic communities that include competition for nutrients, and use quorum sensing to control amensal bacteriocin interactions in a chemostat environment. We computationally explore all two- and three- strain systems, using Bayesian methods to perform model selection, and identify the most robust candidates for producing stable steady state communities. Our findings highlight important interaction motifs that provide stability, and identify requirements for selecting genetic parts and further tuning the community composition.


Assuntos
Algoritmos , Biologia Computacional/métodos , Interações Microbianas/fisiologia , Microbiota/fisiologia , Projetos de Pesquisa , Biologia Sintética/métodos , Teorema de Bayes , Ecossistema , Modelos Biológicos , Percepção de Quorum/fisiologia , Especificidade da Espécie
20.
Methods Mol Biol ; 2210: 207-214, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-32815141

RESUMO

The acquired immunodeficiency syndrome (AIDS) pandemic caused by the human immunodeficiency virus (HIV) is a major global health concern affecting 38 million people worldwide. HIV gene expression is the major determinant of the rate of viral replication leading to the progression of AIDS. The persistence of cellular reservoirs of HIV proviruses, despite prolonged treatment with antiretroviral drugs, represents the main obstacle preventing the eradication of HIV. Epigenetic silencing by histone deacetylase (HDAC) contributes to maintaining HIV transcriptional latency. However, the mechanism of the switch from latency to full HIV replication is unknown. HIV infection and antiretroviral treatment or a combination of both contribute to a higher incidence and severity of periodontitis. Periodontopathic bacteria such as Porphyromonas gingivalis and Fusobacterium nucleatum produce high concentrations of butyric acid, which strongly inhibit HDAC, indicating that periodontitis may mediate the reactivation of HIV replication. Here we describe a stepwise protocol for analyzing HIV reactivation by periodontal pathogens. However, the experiments using HIV requires BSL3 containment, making it difficult to handle HIV in dentistry. Therefore, we present an experimental method using cell lines latently infected with HIV.


Assuntos
Fusobacterium nucleatum/fisiologia , Infecções por HIV/complicações , HIV-1/fisiologia , Periodontite/complicações , Porphyromonas gingivalis/fisiologia , Ativação Viral , Técnicas de Cultura de Células/métodos , Linhagem Celular , Ensaio de Imunoadsorção Enzimática/métodos , Regulação Viral da Expressão Gênica , Infecções por HIV/virologia , HIV-1/genética , Humanos , Immunoblotting/métodos , Interações Microbianas , Periodontite/microbiologia , Reação em Cadeia da Polimerase/métodos , Latência Viral , Replicação Viral
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