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1.
J Crohns Colitis ; 17(2): 277-288, 2023 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-36111848

RESUMO

BACKGROUND AND AIMS: Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. METHODS: We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. RESULTS: MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. CONCLUSIONS: Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.


Assuntos
Colite Ulcerativa , Humanos , Colite Ulcerativa/genética , Estudo de Associação Genômica Ampla , Heterogeneidade Genética , Predisposição Genética para Doença , Fenótipo , Polimorfismo de Nucleotídeo Único , Estudos de Casos e Controles
2.
Biometals ; 35(1): 27-38, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34697758

RESUMO

Iron deficiency is one of the most common nutritional deficiencies worldwide and is often treated with oral iron supplements. However, commonly used supplements, including those based on ferrous iron salts, are associated with gastrointestinal side effects and unfavorable changes in the intestinal microbiome. Sucrosomial® iron is a novel iron formulation that is effective at treating iron deficiency, and with fewer gastrointestinal side effects, yet its effect on the gut microbiome has not been examined previously. Thus, we treated mice for two weeks with diets containing either Sucrosomial® iron or ferrous sulfate as the sole iron source and examined bacterial communities in the intestine using 16S Microbial Profiling of DNA extracted from feces collected both prior to and following dietary treatment. Mice treated with Sucrosomial® iron showed an increase in Shannon diversity over the course of the study. This was associated with a decrease in the abundance of the phylum Proteobacteria, which contains many pathogenic species, and an increase in short chain fatty acid producing bacteria such as Lachnospiraceae, Oscillibacter and Faecalibaculum. None of these changes were observed in mice treated with ferrous sulfate. These results suggest that Sucrosomial® iron may have a beneficial effect on the intestinal microbiome when compared to ferrous sulfate and that this form of iron is a promising alternative to ferrous iron salts for the treatment of iron deficiency.


Assuntos
Anemia Ferropriva , Microbioma Gastrointestinal , Deficiências de Ferro , Anemia Ferropriva/tratamento farmacológico , Animais , Suplementos Nutricionais , Compostos Ferrosos/farmacologia , Ferro , Camundongos , Sais/uso terapêutico
3.
Hum Brain Mapp ; 43(2): 733-749, 2022 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-34811847

RESUMO

There is growing recognition that the composition of the gut microbiota influences behaviour, including responses to threat. The cognitive-interoceptive appraisal of threat-related stimuli relies on dynamic neural computations between the anterior insular (AIC) and the dorsal anterior cingulate (dACC) cortices. If, to what extent, and how microbial consortia influence the activity of this cortical threat processing circuitry is unclear. We addressed this question by combining a threat processing task, neuroimaging, 16S rRNA profiling and computational modelling in healthy participants. Results showed interactions between high-level ecological indices with threat-related AIC-dACC neural dynamics. At finer taxonomic resolutions, the abundance of Ruminococcus was differentially linked to connectivity between, and activity within the AIC and dACC during threat updating. Functional inference analysis provides a strong rationale to motivate future investigations of microbiota-derived metabolites in the observed relationship with threat-related brain processes.


Assuntos
Conectoma , Medo/fisiologia , Microbioma Gastrointestinal/fisiologia , Giro do Cíngulo/fisiologia , Córtex Insular/fisiologia , Rede Nervosa/fisiologia , Adulto , Condicionamento Clássico/fisiologia , Feminino , Giro do Cíngulo/diagnóstico por imagem , Humanos , Córtex Insular/diagnóstico por imagem , Imageamento por Ressonância Magnética , Masculino , Modelos Teóricos , Rede Nervosa/diagnóstico por imagem , RNA Ribossômico 16S , Adulto Jovem
4.
Head Neck ; 43(11): 3324-3330, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34278648

RESUMO

BACKGROUND: Previous microbiome studies of oropharyngeal cancer have shown that there are differences in the oral microbiota between human papillomavirus (HPV)-positive and HPV-negative patients. METHODS: We collected saliva, normal tissue, and tumor biopsies from 13 patients with oropharyngeal cancer (eight HPV-positive, five HPV-negative). We obtained basic clinical data from each patient. Extracted DNA was 16S rRNA gene sequenced. Analysis was based on HPV status and sample site using univariate, multivariate, and mixed effect regression methods. RESULTS: Multivariate analysis methods separated samples based on HPV status (Adonis, p < 0.001). Comparison of patients showed that there were significant changes in microbial richness across all sites based on HPV status (linear mixed effects regression, p = 0.0002). CONCLUSIONS: We found significant differences in overall microbial community and bacterial richness between oropharyngeal patients based on HPV status. Our results suggest that there are significant differences in the microbiome in patients with oropharyngeal cancer based on HPV status.


Assuntos
Microbiota , Neoplasias Orofaríngeas , Infecções por Papillomavirus , DNA Viral/genética , Humanos , Papillomaviridae/genética , Projetos Piloto , RNA Ribossômico 16S/genética , Microambiente Tumoral
5.
Microorganisms ; 9(5)2021 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-33922793

RESUMO

Epidemiological studies link Sarcoptes scabiei infection and impetigo. Scabies mites can promote Streptococcus pyogenes (Group A Streptococcus) and Staphylococcus aureus infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses. However, little is known about the composition and the function of the scabies-associated microbiota. Here, high-throughput whole-metagenome sequencing was used to explore the scabies-associated microbiome. Scabies mites including their immediate microenvironments were isolated from two patients with severe scabies in Northern Australia. Two ~45-50 million paired-end reads Illumina libraries were generated of which ~2 (5.1%) and 0.7 million (1.3%) microbial reads were filtered out by mapping to human (hg19) and mite draft genomes. Taxonomic profiling revealed a microbial community dominated by the phylum Firmicutes (A: 79% and B: 59%) and genera that comprise Streptococcus, Staphylococcus, Acinetobacter, and Corynebacterium. Assembly of the metagenome reads resulted in genome bins representing reference genomes of Acinetobacter baumannii, Streptococcus dysgalactiae (Group C/G), Proteus mirablis and Staphylococcus aureus. The contigs contained genes relevant to pathogenicity and antibiotics resistance. Confocal microscopy of a patient skin sample confirmed A. baumannii, Streptococci and S. aureus in scabies mite gut and faeces and the surrounding skin. The study provides fundamental evidence for the association of opportunistic pathogens with scabies infection.

6.
Front Microbiol ; 12: 613697, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33613484

RESUMO

The normal continuity of skin tissue can be affected by invading pathogens and lead to a series of complicated physiological events. Using an RNA sequencing-based approach, we have captured a metatranscriptomic landscape from diabetic foot infections (DFIs). The hierarchical clustering of the top 2,000 genes showed the expression of four main clusters in DFIs (A, B, C, and D). Clusters A and D were enriched in genes mainly involved in the recruitment of inflammatory cells and immune responses and clusters B and C were enriched in genes related to skin cell development and wound healing processes such as extracellular structure organization and blood vessel development. Differential expression analysis showed more than 500 differentially expressed genes (DEGs) between samples with a low number of virulence factors and samples with a high number of virulence factors. Up-regulated and down-regulated genes were mainly involved in adaptive/native immune responses and transport of mature mRNAs, respectively. Our results demonstrated the importance of inflammatory cytokines of adaptive/native immunity in the progression of DFIs and provided a useful groundwork for capturing gene snapshots in DFIs. In addition, we have provided a general introduction to the challenges and opportunities of RNA sequencing technology in the evaluation of DFIs. Pathways identified in this study such as immune chemokines, Rho GTPases, and corresponding effectors might be important therapeutic targets in the management of DFIs.

7.
Front Microbiol ; 11: 1688, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32793159

RESUMO

Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment.

8.
J Microbiol Methods ; 170: 105856, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32007505

RESUMO

Shotgun metagenomic sequencing or metagenomic whole genome sequencing is a genome-wide sequencing approach to explore bacterial communities directly from their habitat or sites of infection. However, host DNA contamination in metagenomic sequencing overwhelm low biomass of microbial signals and decrease sensitivity for microbial detection. In this study, we evaluated the host DNA depletion efficiency of four different microbiome DNA enrichment methods (NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit and Zymo HostZERO microbial DNA kit) in diabetic foot infection (DFI) tissue samples using quantitative real-time PCR and their effect on bacterial community composition by 16S ribosomal RNA amplicon sequencing. The host DNA depletion ratio (18S/16S rRNA), the percentage of bacterial DNA component and the microbial community profile of DFI were compared before (control) and after each microbiome DNA enrichment method. There was a significant difference in the 18S/16S rRNA ratio among different microbiome DNA enrichment methods (p <.001). QIAamp and HostZERO method reduced 18S/16S rRNA ratio by 32 and 57 fold than control method respectively. The percentage of bacterial DNA component increased more than ten-fold in QiaAmp (71.0 ± 2.7%) and HostZERO (79.9 ± 3.1%) method respectively than those in control method without host DNA depletion (6.7 ± 0.1%). It demonstrated the host DNA contamination was efficiently depleted and bacterial DNA was effectively enriched in HostZERO and QIAamp methods, attesting to the efficacy of these two methods in shotgun metagenomic sequencing studies. Overall, bacterial community composition of DFI samples was similar between control and microbiome enriched DNA samples.


Assuntos
Bactérias/genética , DNA Bacteriano/genética , Pé Diabético/microbiologia , Infecções/diagnóstico , Sequenciamento Completo do Genoma/métodos , Bactérias/classificação , Bactérias/isolamento & purificação , Pé Diabético/patologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Infecções/microbiologia , Metagenômica/métodos , Microbiota/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA/métodos
9.
iScience ; 22: 380-391, 2019 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-31812808

RESUMO

Microbial organisms of the human gut microbiome do not exist in isolation but form complex and diverse interactions to maintain health and reduce risk of disease development. The organization of the gut microbiome is assumed to be a singular assortative network, where interactions between operational taxonomic units (OTUs) can readily be clustered into segregated and distinct communities. Here, we leverage recent methodological advances in network modeling to assess whether communities in the human microbiome exhibit a single network structure or whether co-existing mesoscale network architectures are present. We found evidence for core-periphery structures in the microbiome, supported by strong, assortative community interactions. This complex architecture, coupled with previously reported functional roles of OTUs, provides a nuanced understanding of how the microbiome simultaneously promotes high microbial diversity and maintains functional redundancy.

10.
J Clin Med ; 8(11)2019 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-31717640

RESUMO

Diabetic foot ulcers (DFUs) and diabetic foot infections (DFIs) are associated with reduced patient quality of life, lower-extremity amputation, hospitalization, and high morbidity and mortality. Diverse bacterial communities have been identified in DFUs/DFIs, playing a significant role in infection prognosis. However, due to the high heterogeneity of bacterial communities colonized in DFUs/DFIs, culture-based methods may not isolate all of the bacterial population or unexpected microorganisms. Recently, high sensitivity and specificity of DNA (metagenomics) and RNA (metatranscriptomics) technologies have addressed limitations of culture-based methods and have taken a step beyond bacterial identification. As a consequence, new advances obtained from DNA- and RNA-based techniques for bacterial identification can improve therapeutic approaches. This review evaluated the current state of play in aetiology of DFUs/DFIs on culture and molecular approaches, and discussed the impact of metagenomic and metatranscriptomic methods in bacterial identification approaches.

11.
Sci Rep ; 9(1): 11744, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31409870

RESUMO

Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.


Assuntos
Microbioma Gastrointestinal , Metagenoma , Metagenômica , Microbiota , Sarcoptes scabiei/microbiologia , Streptomyces/genética , Animais , Fezes/microbiologia , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Hibridização in Situ Fluorescente , Metagenômica/métodos , Hipoclorito de Sódio/farmacologia
12.
PLoS Pathog ; 15(1): e1007513, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30673782

RESUMO

Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.


Assuntos
Hibridização Genética/genética , Schistosoma/genética , África , África Ocidental , Animais , Sequência de Bases/genética , Bovinos , Mapeamento Cromossômico/métodos , DNA/genética , Genoma/genética , Genoma Mitocondrial/genética , Hibridização Genética/fisiologia , Oriente Médio , Filogenia , Proteoma/genética , Especificidade da Espécie , Trematódeos/genética , Sequenciamento Completo do Genoma/métodos
13.
J Crohns Colitis ; 13(4): 451-461, 2019 Mar 30.
Artigo em Inglês | MEDLINE | ID: mdl-30445599

RESUMO

BACKGROUND AND AIMS: This study aimed to characterize the mucosa-associated microbiota in ileal Crohn's disease [CD] patients and in healthy controls in terms of host genotype and inflammation status. METHODS: The mucosa-associated microbiotas of intestinal pinch biopsies from 15 ileal CD patients with mild and moderate disease and from 58 healthy controls were analysed based on 16S ribosomal sequencing to determine microbial profile differences between [1] IL23R, NOD2 and ATG16L1 genotypes in healthy subjects, [2] ileal CD patients and control subjects, and [3] inflamed and non-inflamed mucosal tissue in CD patients. RESULTS: The protective variant of the IL23R gene [rs11209026] significantly impacted the microbial composition in the ileum of healthy subjects and was associated with an increased abundance of phylotypes within the family Christensenellaceae as well as increases in diversity and richness. Comparative analysis of healthy and non-inflamed CD microbiome samples indicated a notable decrease in the abundance of Faecalibacterium prausnitzii as well as Shannon diversity and richness. Inflamed and non-inflamed ileal samples of CD subjects had high intra-individual stability and inter-individual variability, but no significant alterations in diversity, richness or taxa were identified. Calprotectin correlated positively with the abundance of Proteobacteria and negatively with diversity in the samples from healthy subjects. CONCLUSIONS: The observation of low diversity and low abundance of beneficial bacteria in healthy control subjects carrying the IL23R [rs11209026] wild-type GG genotype indicates that the gut microbiome is influenced by host genetics and is altered prior to disease diagnosis. Faecal calprotectin may be a potential non-invasive screening tool for dysbiosis in subjects without disorders of intestinal inflammation.


Assuntos
Doença de Crohn/microbiologia , Microbioma Gastrointestinal/genética , Ileíte/microbiologia , Receptores de Interleucina/genética , Adulto , Proteínas Relacionadas à Autofagia/genética , Estudos de Casos e Controles , Doença de Crohn/genética , Doença de Crohn/patologia , Fezes/química , Feminino , Variação Genética , Genótipo , Voluntários Saudáveis , Humanos , Ileíte/genética , Ileíte/patologia , Íleo/microbiologia , Íleo/patologia , Mucosa Intestinal/microbiologia , Mucosa Intestinal/patologia , Complexo Antígeno L1 Leucocitário/análise , Masculino , Pessoa de Meia-Idade , Proteína Adaptadora de Sinalização NOD2/genética , Índice de Gravidade de Doença
14.
Eur J Nutr ; 58(7): 2895-2910, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30324342

RESUMO

PURPOSE: Variation in the human microbiome has been linked with a variety of physiological functions, including immune regulation and metabolism and biosynthesis of vitamins, hormones, and neurotransmitters. Evidence for extraskeletal effects of vitamin D has been accruing and it has been suggested that the effect of vitamin D on health is partially mediated through the microbiome. We aimed to critically evaluate the evidence linking vitamin D and the gastrointestinal microbiome. METHODS: We systematically searched the Embase, Web of Science, PubMed and CINAHL databases, including peer-reviewed publications that reported an association between a measure of vitamin D and the gastrointestinal microbiome in humans or experimental animals. RESULTS: We included 10 mouse and 14 human studies. Mouse studies compared mice fed diets containing different levels of vitamin D (usually high versus low), or vitamin D receptor knockout or Cyp27B1 knockout with wild-type mice. Five mouse studies reported an increase in Bacteroidetes (or taxa within that phylum) in the low vitamin D diet or gene knockout group. Human studies were predominantly observational; all but two of the included studies found some association between vitamin D and the gut microbiome, but the nature of differences observed varied across studies. CONCLUSIONS: Despite substantial heterogeneity, we found evidence to support the hypothesis that vitamin D influences the composition of the gastrointestinal microbiome. However, the research is limited, having been conducted either in mice or in mostly small, selected human populations. Future research in larger population-based studies is needed to fully understand the extent to which vitamin D modulates the microbiome.


Assuntos
Dieta/métodos , Microbioma Gastrointestinal/fisiologia , Vitamina D/sangue , Vitaminas/sangue , Animais , Humanos , Camundongos , Modelos Animais
15.
Gigascience ; 8(1)2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30520948

RESUMO

Background: Foodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Approximately 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available. Results: We sequenced and assembled the genome of P. westermani, which is among the largest of the known pathogen genomes with an estimated size of 1.1 Gb. A 922.8 Mb genome assembly was generated from Illumina and Pacific Biosciences (PacBio) sequence data, covering 84% of the estimated genome size. The genome has a high proportion (45%) of repeat-derived DNA, particularly of the long interspersed element and long terminal repeat subtypes, and the expansion of these elements may explain some of the large size. We predicted 12,852 protein coding genes, showing a high level of conservation with related trematode species. The majority of proteins (80%) had homologs in the human liver fluke Opisthorchis viverrini, with an average sequence identity of 64.1%. Assembly of the P. westermani mitochondrial genome from long PacBio reads resulted in a single high-quality circularized 20.6 kb contig. The contig harbored a 6.9 kb region of non-coding repetitive DNA comprised of three distinct repeat units. Our results suggest that the region is highly polymorphic in P. westermani, possibly even within single worm isolates. Conclusions: The generated assembly represents the first Paragonimus genome sequence and will facilitate future molecular studies of this important, but neglected, parasite group.


Assuntos
Genoma Helmíntico , Paragonimus westermani/genética , Sequenciamento Completo do Genoma/métodos , Animais , Tamanho do Genoma , Genoma Mitocondrial , Sequenciamento de Nucleotídeos em Larga Escala , Anotação de Sequência Molecular , Filogenia , Homologia de Sequência do Ácido Nucleico
16.
Nat Commun ; 9(1): 3728, 2018 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-30214011

RESUMO

Anti-microbial signaling pathways are normally triggered by innate immune receptors when detecting pathogenic microbes to provide protective immunity. Here we show that the inflammasome sensor Nlrp1 aggravates DSS-induced experimental mouse colitis by limiting beneficial, butyrate-producing Clostridiales in the gut. The colitis-protective effects of Nlrp1 deficiency are thus reversed by vancomycin treatment, but recapitulated with butyrate supplementation in wild-type mice. Moreover, an activating mutation in Nlrp1a increases IL-18 and IFNγ production, and decreases colonic butyrate to exacerbate colitis. We also show that, in patients with ulcerative colitis, increased NLRP1 in inflamed regions of the colon is associated with increased IFN-γ. In this context, NLRP1, IL-18 or IFN-γ expression negatively correlates with the abundance of Clostridiales in human rectal mucosal biopsies. Our data identify the NLRP1 inflammasome to be a key negative regulator of protective, butyrate-producing commensals, which therefore promotes inflammatory bowel disease.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas Reguladoras de Apoptose/metabolismo , Butiratos/metabolismo , Clostridiales , Doenças Inflamatórias Intestinais/metabolismo , Interferon gama/metabolismo , Interleucina-18/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/genética , Animais , Proteínas Reguladoras de Apoptose/genética , Colite/metabolismo , Colo/patologia , Feminino , Microbioma Gastrointestinal , Deleção de Genes , Humanos , Inflamassomos , Doenças Inflamatórias Intestinais/tratamento farmacológico , Mucosa Intestinal/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Transgênicos , Proteínas NLR , Reto/metabolismo , Transdução de Sinais , Linfócitos T/citologia , Vancomicina/farmacologia
17.
Parasit Vectors ; 11(1): 301, 2018 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-29769145

RESUMO

BACKGROUND: Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites. We postulated that the SMIPP-Cs have evolved as an adaptation to the parasitic lifestyle of the scabies mite. To formulate testable hypotheses for their functions and to propose possible strategies for translational research we investigated whether the SMIPP-Cs are common to all scabies mite varieties and where within the mite body as well as when throughout the parasitic life-cycle they are expressed. RESULTS: SMIPP-C sequences from human, pig and dog mites were analysed bioinformatically and the phylogenetic relationships between the SMIPP-C multi-copy gene families of human, pig and dog mites were established. Results suggest that amplification of the SMIPP-C genes occurred in a common ancestor and individual genes evolved independently in the different mite varieties. Recombinant human mite SMIPP-C proteins were produced and used for murine polyclonal antibody production. Immunohistology on skin sections from human patients localised the SMIPP-Cs in the mite gut and in mite faeces within in the epidermal skin burrows. SMIPP-C transcription into mRNA in different life stages was assessed in human and pig mites by reverse transcription followed by droplet digital PCR (ddPCR). High transcription levels of SMIPP-C genes were detected in the adult female life stage in comparison to all other life stages. CONCLUSIONS: The fact that the SMIPP-Cs are unique to three Sarcoptes varieties, present in all burrowing life stages and highly expressed in the digestive system of the infective adult female life stage may highlight an essential role in parasitism. As they are excreted from the gut in scybala they presumably are able to interact or interfere with host proteins present in the epidermis.


Assuntos
Cisteína Proteases/genética , Expressão Gênica , Estágios do Ciclo de Vida/genética , Filogenia , Sarcoptes scabiei/enzimologia , Sarcoptes scabiei/genética , Animais , Domínio Catalítico , Biologia Computacional , Cisteína Proteases/metabolismo , Sistema Digestório/enzimologia , Cães , Fezes/parasitologia , Feminino , Interações Hospedeiro-Parasita , Humanos , Camundongos , Proteínas Recombinantes/genética , Proteínas Recombinantes/imunologia , Sarcoptes scabiei/anatomia & histologia , Escabiose/parasitologia , Alinhamento de Sequência , Pele/enzimologia , Pele/imunologia , Suínos
18.
Sci Rep ; 8(1): 4690, 2018 03 16.
Artigo em Inglês | MEDLINE | ID: mdl-29549363

RESUMO

Medically important arboviruses such as dengue, Zika, and chikungunya viruses are primarily transmitted by the globally distributed mosquito Aedes aegypti. Increasing evidence suggests that transmission can be influenced by mosquito viromes. Herein RNA-Seq was used to characterize RNA metaviromes of wild-caught Ae. aegypti from Bangkok (Thailand) and from Cairns (Australia). The two mosquito populations showed a high degree of similarity in their viromes. BLAST searches of assembled contigs suggest up to 27 insect-specific viruses may infect Ae. aegypti, with up to 23 of these currently uncharacterized and up to 16 infecting mosquitoes from both Cairns and Bangkok. Three characterized viruses dominated, Phasi Charoen-like virus, Humaita-Tubiacanga virus and Cell fusing agent virus, and comparisons with other available RNA-Seq datasets suggested infection levels with these viruses may vary in laboratory-reared mosquitoes. As expected, mosquitoes from Bangkok showed higher mitochondrial diversity and carried alleles associated with knock-down resistance to pyrethroids. Blood meal reads primarily mapped to human genes, with a small number also showing homology with rat/mouse and dog genes. These results highlight the wide spectrum of data that can be obtained from such RNA-Seq analyses, and suggests differing viromes may need to be considered in arbovirus vector competence studies.


Assuntos
Aedes/classificação , Vírus de Insetos/classificação , RNA Viral/análise , Análise de Sequência de RNA/métodos , Aedes/efeitos dos fármacos , Aedes/virologia , Animais , Austrália , Bactérias/classificação , Bactérias/genética , Resistência a Medicamentos , Fungos/classificação , Fungos/genética , Vírus de Insetos/genética , Mitocôndrias/genética , Polimorfismo de Nucleotídeo Único , Piretrinas/farmacologia , Especificidade da Espécie , Tailândia
19.
Parasit Vectors ; 10(1): 289, 2017 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-28601087

RESUMO

BACKGROUND: Scabies is one of the most common and widespread parasitic skin infections globally, affecting a large range of mammals including humans, yet the molecular biology of Sarcoptes scabiei is astonishingly understudied. Research has been hampered primarily due to the difficulty of sampling or culturing these obligatory parasitic mites. A further and major impediment to identify and functionally analyse potential therapeutic targets from the recently emerging molecular databases is the lack of appropriate molecular tools. METHODS: We performed standard BLAST based searches of the existing S. scabiei genome databases using sequences of genes described to be involved in RNA interference in Drosophila and the mite model organism Tetranychus urticae. Experimenting with the S. scabiei mu-class glutathione S-transferase (SsGST-mu1) as a candidate gene we explored the feasibility of gene knockdown in S. scabiei by double-stranded RNA-interference (dsRNAi). RESULTS: We provide here an analysis of the existing S. scabiei draft genomes, confirming the presence of a double stranded RNA (dsRNA) - mediated silencing machinery. We report for the first time experimental gene silencing by RNA interference (RNAi) in S. scabiei. Non-invasive immersion of S. scabiei in dsRNA encoding an S. scabiei glutathione S-transferase mu-class 1 enzyme (SsGST-mu1) resulted in a 35% reduction in the transcription of the target gene compared to controls. CONCLUSIONS: A series of experiments identified the optimal conditions allowing systemic experimental RNAi without detrimental side effects on mite viability. This technique can now be used to address the key questions on the fundamental aspects of mite biology and pathogenesis, and to assess the potential therapeutic benefits of silencing S. scabiei target genes.


Assuntos
Entomologia/métodos , Técnicas de Silenciamento de Genes/métodos , Interferência de RNA , Sarcoptes scabiei/genética , Animais , Biologia Computacional , Drosophila/genética , Mamíferos , Tetranychidae/genética
20.
Bioinformatics ; 33(5): 782-783, 2017 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-28025202

RESUMO

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. Availability and Implementation: The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. Contact: l.krause@uq.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Mineração de Dados/métodos , Meio Ambiente , Metagenoma , Microbiota/fisiologia , Software , Humanos , Internet , Microbiota/genética , Plantas , RNA Ribossômico 16S , Estatística como Assunto , Aprendizado de Máquina Supervisionado , Simbiose
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