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1.
Nat Med ; 25(6): 1012-1021, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31142849

RESUMO

The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.


Assuntos
Microbiota , Nascimento Prematuro/microbiologia , Vagina/microbiologia , Adulto , Negro ou Afro-Americano , Biodiversidade , Estudos de Coortes , Citocinas/metabolismo , Feminino , Interações entre Hospedeiro e Microrganismos/imunologia , Humanos , Recém-Nascido , Mediadores da Inflamação/metabolismo , Estudos Longitudinais , Metagenômica , Microbiota/genética , Microbiota/imunologia , Nascimento Prematuro/etiologia , Nascimento Prematuro/imunologia , Fatores de Risco , Estados Unidos , Vagina/imunologia , Adulto Jovem
2.
Nat Med ; 25(6): 1001-1011, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31142850

RESUMO

The microbiome of the female reproductive tract has implications for women's reproductive health. We examined the vaginal microbiome in two cohorts of women who experienced normal term births: a cross-sectionally sampled cohort of 613 pregnant and 1,969 non-pregnant women, focusing on 300 pregnant and 300 non-pregnant women of African, Hispanic or European ancestry case-matched for race, gestational age and household income; and a longitudinally sampled cohort of 90 pregnant women of African or non-African ancestry. In these women, the vaginal microbiome shifted during pregnancy toward Lactobacillus-dominated profiles at the expense of taxa often associated with vaginal dysbiosis. The shifts occurred early in pregnancy, followed predictable patterns, were associated with simplification of the metabolic capacity of the microbiome and were significant only in women of African or Hispanic ancestry. Both genomic and environmental factors are likely contributors to these trends, with socioeconomic status as a likely environmental influence.


Assuntos
Microbiota , Gravidez/fisiologia , Vagina/microbiologia , Adulto , Negro ou Afro-Americano , Biodiversidade , Estudos de Coortes , Estudos Transversais , Feminino , Hispânico ou Latino , Interações entre Hospedeiro e Microrganismos/genética , Interações entre Hospedeiro e Microrganismos/fisiologia , Humanos , Microbiota/genética , Microbiota/fisiologia , Classe Social , População Branca
3.
BMC Genomics ; 19(1): 770, 2018 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-30355302

RESUMO

BACKGROUND: Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli and T. conorhini represent clades that are phylogenetically closely related to the T. cruzi and T. cruzi-like taxa and provide insights into the evolution of pathogenicity in those parasites. T. rangeli, like T. cruzi is endemic in many Latin American countries, whereas T. conorhini is tropicopolitan. T. rangeli and T. conorhini are exclusively extracellular, while T. cruzi has an intracellular stage in the mammalian host. RESULTS: Here we provide the first comprehensive sequence analysis of T. rangeli AM80 and T. conorhini 025E, and provide a comparison of their genomes to those of T. cruzi G and T. cruzi CL, respectively members of T. cruzi lineages TcI and TcVI. We report de novo assembled genome sequences of the low-virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E ranging from ~ 21-25 Mbp, with ~ 10,000 to 13,000 genes, and for the highly virulent and hybrid T. cruzi CL we present a ~ 65 Mbp in-house assembled haplotyped genome with ~ 12,500 genes per haplotype. Single copy orthologs of the two T. cruzi strains exhibited ~ 97% amino acid identity, and ~ 78% identity to proteins of T. rangeli or T. conorhini. Proteins of the latter two organisms exhibited ~ 84% identity. T. cruzi CL exhibited the highest heterozygosity. T. rangeli and T. conorhini displayed greater metabolic capabilities for utilization of complex carbohydrates, and contained fewer retrotransposons and multigene family copies, i.e. trans-sialidases, mucins, DGF-1, and MASP, compared to T. cruzi. CONCLUSIONS: Our analyses of the T. rangeli and T. conorhini genomes closely reflected their phylogenetic proximity to the T. cruzi clade, and were largely consistent with their divergent life cycles. Our results provide a greater context for understanding the life cycles, host range expansion, immunity evasion, and pathogenesis of these trypanosomatids.


Assuntos
Genoma de Protozoário , Genômica , Trypanosoma cruzi/genética , Trypanosoma rangeli/genética , Trypanosoma/genética , Biologia Computacional/métodos , Metabolismo Energético/genética , Genômica/métodos , Genótipo , Tipagem Molecular , Família Multigênica , Filogenia , Pseudogenes , Trypanosoma/classificação , Trypanosoma/metabolismo , Trypanosoma/patogenicidade , Trypanosoma cruzi/classificação , Trypanosoma cruzi/metabolismo , Trypanosoma cruzi/patogenicidade , Trypanosoma rangeli/classificação , Trypanosoma rangeli/metabolismo , Trypanosoma rangeli/patogenicidade , Virulência/genética
4.
J Mol Evol ; 84(2-3): 104-115, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28210761

RESUMO

We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico. The alignments indicated that the genes are homologous with a high degree of confidence, and three-dimensional structural models strongly supported a functional relationship to previously characterized AGO1, DCL1, and DCL2 proteins. Phylogenetic analysis of these putative proteins showed that these genes, when present, evolved in parallel with other nuclear genes, arguing that the RNAi system genes share a common progenitor, likely across all Kinetoplastea. In addition, the genome segments bearing these genes are highly conserved and syntenic, even among those taxa in which they are absent. However, taxa in which these genes are apparently absent represent several widely divergent branches of kinetoplastids, arguing that these genes were independently lost at least six times in the evolutionary history of these organisms. The mechanisms responsible for the apparent coordinate loss of these RNAi system genes independently in several lineages of kinetoplastids, while being maintained in other related lineages, are currently unknown.


Assuntos
Crithidia fasciculata/genética , DNA de Cinetoplasto/genética , Leishmania braziliensis/genética , Trypanosomatina/genética , Sequência de Aminoácidos/genética , Proteínas Argonautas/genética , Evolução Biológica , DNA de Cinetoplasto/metabolismo , Eucariotos/genética , Evolução Molecular , Genoma/genética , Filogenia , Interferência de RNA/fisiologia , Ribonuclease III/genética , Alinhamento de Sequência/métodos , Sintenia/genética
5.
Sci Rep ; 5: 16324, 2015 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-26549794

RESUMO

Cryptosporidium parvum and C. hominis are the most relevant species of this genus for human health. Both cause a self-limiting diarrhea in immunocompetent individuals, but cause potentially life-threatening disease in the immunocompromised. Despite the importance of these pathogens, only one reference genome of each has been analyzed and published. These two reference genomes were sequenced using automated capillary sequencing; as of yet, no next generation sequencing technology has been applied to improve their assemblies and annotations. For C. hominis, the main challenge that prevents a larger number of genomes to be sequenced is its resistance to axenic culture. In the present study, we employed next generation technology to analyse the genomic DNA and RNA to generate a new reference genome sequence of a C. hominis strain isolated directly from human stool and a new genome annotation of the C. parvum Iowa reference genome.


Assuntos
Criptosporidiose/parasitologia , Cryptosporidium/classificação , Cryptosporidium/genética , Genoma de Protozoário , Biologia Computacional/métodos , Cryptosporidium parvum/genética , Bases de Dados Genéticas , Ontologia Genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Anotação de Sequência Molecular , Tipagem Molecular , Filogenia
6.
Genome Biol Evol ; 5(2): 338-50, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23345457

RESUMO

It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.


Assuntos
Betaproteobacteria/genética , RNA Ribossômico 16S/genética , Simbiose/genética , Trypanosomatina/genética , Animais , Betaproteobacteria/metabolismo , Genoma Bacteriano , Dados de Sequência Molecular , Filogenia , Trypanosomatina/crescimento & desenvolvimento , Trypanosomatina/metabolismo , Trypanosomatina/microbiologia
7.
PLoS One ; 6(8): e23518, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21853145

RESUMO

It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.


Assuntos
Bactérias/genética , Genes Bacterianos/genética , Genes de Protozoários/genética , Heme/biossíntese , Filogenia , Simbiose/genética , Trypanosomatina/genética , Animais , Vias Biossintéticas/genética , DNA de Cinetoplasto/genética , Funções Verossimilhança , Trypanosomatina/microbiologia
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