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1.
Curr Opin Microbiol ; 54: 119-126, 2020 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-32114367

RESUMO

Relationships between hosts and host-associated microbial communities are complex, intimate, and associated with a wide variety of health and disease states. For these reasons, these relationships have raised many difficult questions and claims about microbiome causation. While philosophers and scientists alike have pondered the challenges of causal inference and offered postulates and rules, there are no simple solutions, especially with poorly characterized, putative causal factors such as microbiomes, ill-defined host effects, and inadequate experimental models. Recommendations are provided here for conceptual and experimental approaches regarding microbiome causal inference, and for a research agenda.

2.
Semin Immunopathol ; 2020 Feb 04.
Artigo em Inglês | MEDLINE | ID: mdl-32020337

RESUMO

Preterm birth is the leading cause of mortality in children under the age of five worldwide. Despite major efforts, we still lack the ability to accurately predict and effectively prevent preterm birth. While multiple factors contribute to preterm labor, dysregulations of immunological adaptations required for the maintenance of a healthy pregnancy is at its pathophysiological core. Consequently, a precise understanding of these chronologically paced immune adaptations and of the biological pacemakers that synchronize the pregnancy "immune clock" is a critical first step towards identifying deviations that are hallmarks of peterm birth. Here, we will review key elements of the fetal, placental, and maternal pacemakers that program the immune clock of pregnancy. We will then emphasize multiomic studies that enable a more integrated view of pregnancy-related immune adaptations. Such multiomic assessments can strengthen the biological plausibility of immunological findings and increase the power of biological signatures predictive of preterm birth.

3.
Nature ; 578(7795): 425-431, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-32051592

RESUMO

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

4.
Periodontol 2000 ; 82(1): 26-41, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31850642

RESUMO

In humans, the composition of microbial communities differs among body sites and between habitats within a single site. Patterns of variation in the distribution of organisms across time and space are referred to as "biogeography." The human oral cavity is a critical observatory for exploring microbial biogeography because it is spatially structured, easily accessible, and its microbiota has been linked to the promotion of both health and disease. The biogeographic features of microbial communities residing in spatially distinct, but ecologically similar, environments on the human body, including the subgingival crevice, have not yet been adequately explored. The purpose of this paper is twofold. First, we seek to provide the dental community with a primer on biogeographic theory, highlighting its relevance to the study of the human oral cavity. We summarize what is known about the biogeographic variation of dental caries and periodontitis and postulate that disease occurrence reflects spatial patterning in the composition and structure of oral microbial communities. Second, we present a number of methods that investigators can use to test specific hypotheses using biogeographic theory. To anchor our discussion, we apply each method to a case study and examine the spatial variation of the human subgingival microbiota in 2 individuals. Our case study suggests that the composition of subgingival communities may conform to an anterior-to-posterior gradient within the oral cavity. The gradient appears to be structured by both deterministic and nondeterministic processes, although additional work is needed to confirm these findings. A better understanding of biogeographic patterns and processes will lead to improved efficacy of dental interventions targeting the oral microbiota.

5.
Nat Microbiol ; 5(2): 343-353, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31873203

RESUMO

Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.

6.
Front Microbiol ; 10: 2291, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31649637

RESUMO

Iron overload disorder (IOD) affects many wildlife species cared for ex situ. Two of the four rhinoceros species in human care, Sumatran rhinoceros (Dicerorhinus sumatrensis) and black rhinoceros (Diceros bicornis), are susceptible, whereas the other two, white rhinoceros (Ceratotherium simum) and greater one-horned (GOH) rhinoceros (Rhinoceros unicornis), are relatively resistant to IOD. Complex interrelationships exist between mammalian hosts, their indigenous gut microbiota, metabolome, physical condition, and iron availability. The goal of this study was to gain insight into these relationships within the family Rhinocerotidae. Specific objectives were to (1) characterize the gut microbiome and metabolome of four rhinoceros species; (2) compare the microbiome and metabolome of IOD-susceptible and IOD-resistant rhinoceros species; and (3) identify variation in the microbiome and metabolome associated with compromised health or disease in IOD-susceptible rhinoceroses. Fecal samples were collected from 31 rhinoceroses (Sumatran rhinoceros, n = 3; black rhinoceros, n = 6; GOH rhinoceros, n = 9; white rhinoceros, n = 13) located at five facilities, and matched fecal aliquots were processed for microbiome and metabolome analyses using 16S rRNA gene sequencing and nuclear magnetic resonance spectroscopy, respectively. Despite the phylogenetic disparity and dissimilar zoo diets of the hosts, the structure of the fecal microbiota of the two IOD-susceptible rhinoceros species were more closely related to each other than to those of the two IOD-resistant species (Bray-Curtis dissimilarity; IOD-susceptible vs. IOD-resistant p-value < 0.001). In addition, IOD-susceptible rhinoceroses exhibited less microbial diversity than their IOD-resistant relatives (Shannon diversity; p-value < 0.001) which could have health implications. Of note, the black rhinoceros was distinct among the four rhinoceros species with the most divergent fecal metabolome; interestingly, it contained higher concentrations of short chain fatty acids. Neither age nor sex were associated with differences in microbial community composition (p = 0.253 and 0.488, respectively) or fecal metabolomic profile (p = 0.634 and 0.332, respectively). Differences in the distal gut microbiomes between IOD-resistant and IOD-susceptible rhinoceroses support hypotheses that gut microbes play a role in host iron acquisition, and further studies and experiments to test these hypotheses are warranted.

7.
Immunity ; 51(2): 211-213, 2019 08 20.
Artigo em Inglês | MEDLINE | ID: mdl-31433968

RESUMO

In a recent issue of Nature Medicine, Gopalakrishna et al. show that altered patterns of IgA binding to gut bacteria in premature infants are associated with necrotizing enterocolitis, underscoring the critical role of host mucosal immunity in shaping the microbiota.


Assuntos
Enterocolite Necrosante , Microbiota , Criança , Pré-Escolar , Humanos , Imunidade nas Mucosas , Imunoglobulina A , Lactente , Recém-Nascido , Recém-Nascido Prematuro
8.
Inflamm Bowel Dis ; 25(12): 1927-1938, 2019 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-31276165

RESUMO

BACKGROUND: The beneficial effects of antibiotics in Crohn's disease (CD) depend in part on the gut microbiota but are inadequately understood. We investigated the impact of metronidazole (MET) and metronidazole plus azithromycin (MET+AZ) on the microbiota in pediatric CD and the use of microbiota features as classifiers or predictors of disease remission. METHODS: 16S rRNA-based microbiota profiling was performed on stool samples from 67 patients in a multinational, randomized, controlled, longitudinal, 12-week trial of MET vs MET+AZ in children with mild to moderate CD. Profiles were analyzed together with disease activity, and then used to construct random forest models to classify remission or predict treatment response. RESULTS: Both MET and MET+AZ significantly decreased diversity of the microbiota and caused large treatment-specific shifts in microbiota structure at week 4. Disease remission was associated with a treatment-specific microbiota configuration. Random forest models constructed from microbiota profiles before and during antibiotic treatment with metronidazole accurately classified disease remission in this treatment group (area under the curve [AUC], 0.879; 95% confidence interval, 0.683-0.9877; sensitivity, 0.7778; specificity, 1.000; P < 0.001). A random forest model trained on pre-antibiotic microbiota profiles predicted disease remission at week 4 with modest accuracy (AUC, 0.8; P = 0.24). CONCLUSIONS: MET and MET+AZ antibiotic regimens in pediatric CD lead to distinct gut microbiota structures at remission. It may be possible to classify and predict remission based in part on microbiota profiles, but larger cohorts will be needed to realize this goal.

9.
J Perinatol ; 39(3): 354-358, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30560947

RESUMO

Based upon our recent insights into the determinants of preterm birth, which is the leading cause of death in children under five years of age worldwide, we describe potential analytic frameworks that provides both a common understanding and, ultimately the basis for effective, ameliorative action. Our research on preterm birth serves as an example that the framing of any human health condition is a result of complex interactions between the genome and the exposome. New discoveries of the basic biology of pregnancy, such as the complex immunological and signaling processes that dictate the health and length of gestation, have revealed a complexity in the interactions (current and ancestral) between genetic and environmental forces. Understanding of these relationships may help reduce disparities in preterm birth and guide productive research endeavors and ultimately, effective clinical and public health interventions.

10.
Bioinformatics ; 35(1): 95-103, 2019 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30561547

RESUMO

Motivation: Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia. Results: We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified. Availability and implementation: Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Metaboloma , Microbiota , Gravidez , Proteoma , Transcriptoma , Biologia Computacional , Feminino , Humanos
11.
Microbiome ; 6(1): 226, 2018 12 17.
Artigo em Inglês | MEDLINE | ID: mdl-30558668

RESUMO

BACKGROUND: The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam ( https://github.com/benjjneb/decontam ), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls. RESULTS: Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants. CONCLUSIONS: Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.


Assuntos
Bactérias/genética , Marcadores Genéticos , Metagenômica/métodos , Boca/microbiologia , Análise de Sequência de DNA/métodos , Bactérias/classificação , Contaminação por DNA , DNA Bacteriano/genética , DNA Ribossômico/genética , Bases de Dados Genéticas , Humanos , Internet , Modelos Estatísticos , RNA Ribossômico 16S/genética , Software
12.
Proc Natl Acad Sci U S A ; 115(51): 12902-12910, 2018 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-30559176

RESUMO

Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.


Assuntos
Anti-Infecciosos/farmacologia , Controle de Doenças Transmissíveis/métodos , Resistência Microbiana a Medicamentos/efeitos dos fármacos , Microbiota/efeitos dos fármacos , Vacinas/uso terapêutico , Doenças Transmissíveis/tratamento farmacológico , Resistência Microbiana a Medicamentos/genética , Interações entre Hospedeiro e Microrganismos/efeitos dos fármacos , Interações entre Hospedeiro e Microrganismos/genética , Interações entre Hospedeiro e Microrganismos/imunologia , Humanos
13.
Genome Res ; 28(10): 1467-1480, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30232199

RESUMO

Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.


Assuntos
Bactérias/classificação , Trato Gastrointestinal/microbiologia , Metagenômica/métodos , Análise de Sequência de DNA/métodos , Vagina/microbiologia , Bactérias/genética , Mapeamento de Sequências Contíguas , DNA Bacteriano/genética , DNA Ribossômico/genética , Feminino , Humanos , Estudos Longitudinais , Filogenia , Gravidez , Resultado da Gravidez , RNA Ribossômico 16S/genética
14.
J Infect Dis ; 218(12): 1911-1921, 2018 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-30010906

RESUMO

Background: Several promising live attenuated dengue vaccines are in development, but information about innate immune responses and early correlates of protection is lacking. Methods: We characterized human genome-wide transcripts in whole blood from 10 volunteers at 11 time points after immunization with the dengue virus type 3 (DENV-3) component of the National Institutes of Health dengue vaccine candidate TV003 and from 30 hospitalized children with acute primary DENV-3 infection. We compared day-specific gene expression patterns with subsequent neutralizing antibody (NAb) titers. Results: The transcriptional response to vaccination was largely confined to days 5-20 and was dominated by an interferon-associated signature and a cell cycle signature that peaked on days 8 and 14, respectively. Changes in transcript abundance were much greater in magnitude and scope in symptomatic natural infection than following vaccination (maximum fold-change >200 vs 21 postvaccination; 3210 vs 286 transcripts with significant fold-change), but shared gene modules were induced in the same sequence. The abundances of 131 transcripts on days 8 and 9 postvaccination were strongly correlated with NAb titers measured 6 weeks postvaccination. Conclusions: Live attenuated dengue vaccination elicits early transcriptional responses that mirror those found in symptomatic natural infection and provide candidate early markers of protection against DENV infection. Clinical Trials Registration: NCT00831012.


Assuntos
Anticorpos Neutralizantes/sangue , Anticorpos Antivirais/sangue , Vacinas contra Dengue/imunologia , Dengue/prevenção & controle , Regulação Viral da Expressão Gênica/imunologia , Adolescente , Adulto , Dengue/sangue , Dengue/imunologia , Humanos , Masculino , Pessoa de Meia-Idade , Fatores de Tempo , Transcrição Genética/imunologia , Vacinação , Vacinas Atenuadas/imunologia , Adulto Jovem
15.
Emerg Infect Dis ; 24(8): 1490-1496, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30014842

RESUMO

The decreasing effectiveness of antimicrobial agents is a global public health threat, yet risk factors for community-acquired antimicrobial resistance (CA-AMR) in low-income settings have not been clearly elucidated. Our aim was to identify risk factors for CA-AMR with extended-spectrum ß-lactamase (ESBL)-producing organisms among urban-dwelling women in India. We collected microbiological and survey data in an observational study of primigravidae women in a public hospital in Hyderabad, India. We analyzed the data using multivariate logistic and linear regression and found that 7% of 1,836 women had bacteriuria; 48% of isolates were ESBL-producing organisms. Women in the bottom 50th percentile of income distribution were more likely to have bacteriuria (adjusted odds ratio 1.44, 95% CI 0.99-2.10) and significantly more likely to have bacteriuria with ESBL-producing organisms (adjusted odds ratio 2.04, 95% CI 1.17-3.54). Nonparametric analyses demonstrated a negative relationship between the prevalence of ESBL and income.


Assuntos
Infecções Bacterianas/epidemiologia , Infecções Bacterianas/microbiologia , Infecções Comunitárias Adquiridas/epidemiologia , Infecções Comunitárias Adquiridas/microbiologia , Farmacorresistência Bacteriana Múltipla , Pobreza , Adolescente , Adulto , Antibacterianos/farmacologia , Bacteriúria/epidemiologia , Bacteriúria/microbiologia , Estudos Transversais , Feminino , Humanos , Índia/epidemiologia , Gravidez , Fatores de Risco , Adulto Jovem
17.
Nat Commun ; 9(1): 681, 2018 02 14.
Artigo em Inglês | MEDLINE | ID: mdl-29445174

RESUMO

Spatial and temporal patterns in microbial communities provide insights into the forces that shape them, their functions and roles in health and disease. Here, we used spatial and ecological statistics to analyze the role that saliva plays in structuring bacterial communities of the human mouth using >9000 dental and mucosal samples. We show that regardless of tissue type (teeth, alveolar mucosa, keratinized gingiva, or buccal mucosa), surface-associated bacterial communities vary along an ecological gradient from the front to the back of the mouth, and that on exposed tooth surfaces, the gradient is pronounced on lingual compared to buccal surfaces. Furthermore, our data suggest that this gradient is attenuated in individuals with low salivary flow due to Sjögren's syndrome. Taken together, our findings imply that salivary flow influences the spatial organization of microbial communities and that biogeographical patterns may be useful for understanding host physiological processes and for predicting disease.


Assuntos
Bactérias/crescimento & desenvolvimento , Boca/microbiologia , Saliva/microbiologia , Salivação , Adulto , Idoso , Bactérias/classificação , Bactérias/genética , Biodiversidade , Feminino , Variação Genética , Humanos , Masculino , Pessoa de Meia-Idade , Mucosa Bucal/microbiologia , RNA Ribossômico 16S/genética , Saliva/metabolismo , Síndrome de Sjogren/complicações , Síndrome de Sjogren/microbiologia , Língua/microbiologia , Dente/microbiologia , Xerostomia/etiologia , Xerostomia/microbiologia , Adulto Jovem
18.
Nat Rev Gastroenterol Hepatol ; 15(4): 197-205, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29362469

RESUMO

Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.


Assuntos
Microbioma Gastrointestinal/fisiologia , Biodiversidade , Evolução Biológica , Desenvolvimento Infantil/fisiologia , Feminino , Deriva Genética , Interações entre Hospedeiro e Microrganismos/fisiologia , Humanos , Lactente , Recém-Nascido , Trabalho de Parto/fisiologia , Troca Materno-Fetal/fisiologia , Gravidez/fisiologia , Seleção Genética/fisiologia , Fatores de Tempo
20.
Nat Microbiol ; 3(1): 8-16, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29255284

RESUMO

Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept.


Assuntos
Bactérias/classificação , Microbioma Gastrointestinal/genética , Trato Gastrointestinal/microbiologia , Metagenoma , Animais , Bactérias/genética , Técnicas de Tipagem Bacteriana , Biodiversidade , Humanos , Metagenômica , RNA Ribossômico 16S/genética
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