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1.
Sci Rep ; 11(1): 8922, 2021 04 26.
Artículo en Inglés | MEDLINE | ID: mdl-33903709

RESUMEN

The coronavirus disease 2019 (COVID-19) has rapidly spread around the world, impacting the lives of many individuals. Growing evidence suggests that the nasopharyngeal and respiratory tract microbiome are influenced by various health and disease conditions, including the presence and the severity of different viral disease. To evaluate the potential interactions between Severe Acute Respiratory Syndrome Corona 2 (SARS-CoV-2) and the nasopharyngeal microbiome. Microbial composition of nasopharyngeal swab samples submitted to the clinical microbiology lab for suspected SARS-CoV-2 infections was assessed using 16S amplicon sequencing. The study included a total of 55 nasopharyngeal samples from 33 subjects, with longitudinal sampling available for 12 out of the 33 subjects. 21 of the 33 subjects had at least one positive COVID-19 PCR results as determined by the clinical microbiology lab. Inter-personal variation was the strongest factor explaining > 75% of the microbial variation, irrespective of the SARS-CoV-2 status. No significant effect of SARS-CoV-2 on the nasopharyngeal microbial community was observed using multiple analysis methods. These results indicate that unlike some other viruses, for which an effect on the microbial composition was noted, SARS-CoV-2 does not have a strong effect on the nasopharynx microbial habitants.


Asunto(s)
/microbiología , Microbiota , Nasofaringe/microbiología , /fisiología , Adulto , Anciano , Femenino , Humanos , Masculino , Microbiota/genética , Persona de Mediana Edad , ARN Ribosómico 16S/genética
2.
Huan Jing Ke Xue ; 42(5): 2541-2549, 2021 May 08.
Artículo en Chino | MEDLINE | ID: mdl-33884825

RESUMEN

The widespread use of antibiotics in the aquaculture industry has caused antibiotic resistance genes (ARGs) pollution. Metagenomics technology was used to detect and analyze the relative abundance of ARGs and microbial community structure in a fishery reclamation mining subsidence area. A total of 29 ARGs were detected, and bacA had the highest relative abundance in all the samples, reaching 1.96×10-5-1.19×10-4. The relative abundance of sulfonamide and tetracycline ARGs in sediments was relatively high and the relative abundance of multidrug ARGs in well water was relatively high. Proteobacteria was the most dominant bacterial phylum in all the samples, and Chloroflexi and Euryarchaeota were relatively abundant in the sediments. Thiobacillus was the most dominant bacterial genus in the sediments, and Acinetobacter and Pseudomonas were the dominant bacterial genera in the well water. The correlation analysis between the ARGs and microorganisms showed that the genera and ARGs were mainly correlated to a moderate degree, and multiple genera had significant positive correlations with ARGs. The distribution of ARGs was affected by the structure of the microbial community. The sediments and well water in the fishery reclamation mining subsidence area were both contaminated by ARGs, and corresponding control measures should be strengthened to protect the regional environment.


Asunto(s)
Antibacterianos , Microbiota , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Explotaciones Pesqueras , Genes Bacterianos/genética , Microbiota/genética
3.
Nat Commun ; 12(1): 2009, 2021 03 31.
Artículo en Inglés | MEDLINE | ID: mdl-33790294

RESUMEN

Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.


Asunto(s)
Genoma Bacteriano/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenoma/genética , Metagenómica/métodos , ARN Ribosómico 16S/genética , Aguas del Alcantarillado/microbiología , Bacterias/clasificación , Bacterias/genética , Reactores Biológicos/microbiología , Dinamarca , Microbiota/genética , Filogenia , ARN Ribosómico 23S/genética , ARN Ribosómico 5S/genética , Aguas Residuales/microbiología , Purificación del Agua/métodos
4.
Nat Commun ; 12(1): 2126, 2021 04 09.
Artículo en Inglés | MEDLINE | ID: mdl-33837203

RESUMEN

There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.


Asunto(s)
Rechazo de Injerto/microbiología , Trasplante de Pulmón/efectos adversos , Pulmón/microbiología , Microbiota/inmunología , Neumonía Bacteriana/microbiología , Adulto , Aloinjertos/inmunología , Aloinjertos/microbiología , Bacterias/genética , Bacterias/inmunología , Bacterias/aislamiento & purificación , Bacterias/patogenicidad , Carga Bacteriana/inmunología , Técnicas Bacteriológicas , Líquido del Lavado Bronquioalveolar/microbiología , Broncoscopía , ADN Bacteriano/aislamiento & purificación , Femenino , Rechazo de Injerto/diagnóstico , Rechazo de Injerto/inmunología , Humanos , Tolerancia Inmunológica , Estudios Longitudinales , Pulmón/inmunología , Masculino , Metagenómica , Microbiota/genética , Persona de Mediana Edad , Neumonía Bacteriana/diagnóstico , Neumonía Bacteriana/inmunología , Estudios Prospectivos , ARN Ribosómico 16S/genética
5.
BMC Infect Dis ; 21(1): 373, 2021 Apr 21.
Artículo en Inglés | MEDLINE | ID: mdl-33882835

RESUMEN

BACKGROUND: Aberrant microbiota composition has been linked to disease development at numerous anatomical sites. Microbiota changes in reaction to viral infections, such as human papillomavirus (HPV), have been investigated almost exclusively in the female reproductive tract. However, HPV infection may also affect male health by reducing semen quality and fertility. The aim of this study was to investigate whether present HPV DNA is associated with detectable changes in semen bacterial microbiota composition and diversity. METHODS: This study relied on stored semen samples from 31 fertile healthy men who participated in the Finnish family HPV Study during the years 1998-2001. DNA was extracted from semen with PCR template preparation kit. HPV was genotyped using Luminex-based Multimetrix® assay. Microbiota was analyzed from the V3-V4 region of 16S rDNA gene following sequencing on an Illumina MiSeq platform. All statistical analyses were performed with Calypso software version 8.84. RESULTS: HPV DNA was detected in 19.4% (6/31) of the semen samples. HPV status in the semen did not impact the α-diversity estimations, as measured by Chao1 and Shannon indices, nor ß-diversity. Nevertheless, HPV-positive semen samples exhibited differences in the taxonomic composition of the bacterial microbiota including higher abundances of Moraxellaceae (p = 0.028), Streptococcus (p = 0.0058) and Peptostreptococcus (p = 0.012) compared to HPV-negative semen samples. CONCLUSION: HPV infection is associated with altered bacterial microbiota composition in semen, and this might have in impact to male health in general. As of present, it is unclear whether these changes result from HPV infection or whether altered bacterial microbiota increases susceptibility to HPV infection. More research is needed on viral-bacterial interactions in the male reproductive system.


Asunto(s)
Bacterias/genética , Microbiota/genética , Papillomaviridae/genética , Infecciones por Papillomavirus/epidemiología , Semen/microbiología , Adulto , ADN Ribosómico/genética , ADN Viral/genética , Femenino , Finlandia/epidemiología , Genotipo , Voluntarios Sanos , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Infecciones por Papillomavirus/virología , Reacción en Cadena de la Polimerasa , Análisis de Semen , Adulto Joven
6.
Int J Mol Sci ; 22(7)2021 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-33805379

RESUMEN

ß-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of ß-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 ß-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial ß-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant ß-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of ß-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.


Asunto(s)
Antozoos/microbiología , Bacterias/enzimología , Microbiota/genética , beta-Glucosidasa/genética , Animales , Bacterias/genética , Metagenómica , Filogenia , beta-Glucosidasa/metabolismo
7.
Microbiome ; 9(1): 68, 2021 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-33752735

RESUMEN

BACKGROUND: An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS: Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS: Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.


Asunto(s)
Microbioma Gastrointestinal , Microbiota , Animales , Femenino , Microbioma Gastrointestinal/genética , Macaca mulatta , Ratones , Microbiota/genética , Puerto Rico , ARN Ribosómico 16S/genética
8.
Microbiome ; 9(1): 69, 2021 03 24.
Artículo en Inglés | MEDLINE | ID: mdl-33762001

RESUMEN

Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets-referred to here as holo-omics-provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness. Video abstract.


Asunto(s)
Microbiota , Microbiota/genética , Plantas
9.
Microbiome ; 9(1): 74, 2021 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-33771219

RESUMEN

BACKGROUND: While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms. METHODS: Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. RESULTS: We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism. CONCLUSIONS: Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms. TRIAL REGISTRATION: This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010. Video abstract.


Asunto(s)
Microbioma Gastrointestinal , Síndrome del Colon Irritable , Microbiota , Animales , Dieta , Microbioma Gastrointestinal/genética , Humanos , Hidrógeno , Microbiota/genética
10.
Microbiome ; 9(1): 75, 2021 03 26.
Artículo en Inglés | MEDLINE | ID: mdl-33771222

RESUMEN

BACKGROUND: Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson's disease (PD) and Alzheimer's disease (AD) or as a "brain microbiome" in the context of healthy patients' brain samples. METHODS: Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. RESULTS: Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue's sterility and could also be found in independent brain 16S rRNA gene sequences. CONCLUSIONS: Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains. Video abstract.


Asunto(s)
Microbiota , Enfermedad de Parkinson , Animales , Bacterias/genética , Encéfalo , ADN Bacteriano/genética , Humanos , Ratones , Microbiota/genética , ARN Ribosómico 16S/genética
11.
Microbiome ; 9(1): 76, 2021 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-33775256

RESUMEN

BACKGROUND: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data. RESULTS: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface. CONCLUSIONS: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.


Asunto(s)
Microbiota , Programas Informáticos , Interpretación Estadística de Datos , Humanos , Metagenómica , Microbiota/genética , ARN Ribosómico 16S/genética
12.
Microbiome ; 9(1): 79, 2021 03 29.
Artículo en Inglés | MEDLINE | ID: mdl-33781324

RESUMEN

BACKGROUND: Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. RESULTS: We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. CONCLUSION: We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.


Asunto(s)
Metagenoma , Microbiota , Humanos , Metagenómica , Microbiota/genética , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
13.
An Acad Bras Cienc ; 93(2): e20200945, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33681877

RESUMEN

Bacterial vaginosis (BV) has been considered as dysbiosis state whose etiology is not fully understood. This condition affects a large number of women of reproductive age and its study has been highly relevant due to the growing association of BV with and gynecological and obstetric complications and diseases, in addition to a greater susceptibility to sexually transmitted diseases, including HIV. The vaginal microbiota composition presents high variability among different ethnic groups of women, although, generally, the prevalence of lactobacilli species has been reported. Several studies suggest they may play a protective role, especially Lactobacillus crispatus whose population is typically present in low proportions in women with BV. This review article describes the contributions and limitations of genomic approaches in elucidating protective characteristics and mechanisms associated with colonization and persistence of lactobacilli strains. Although some genetic features were associated with resilience of L. crispatus during BV, furher studies are required to uncover their functions.


Asunto(s)
Microbiota , Vaginosis Bacteriana , Femenino , Genómica , Humanos , Lactobacillus/genética , Microbiota/genética , Vaginosis Bacteriana/genética
14.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33734952

RESUMEN

Introduction. Oral tissues are generally homeostatic despite exposure to many potential inflammatory agents including the resident microbiota. This requires the balancing of inflammation by regulatory mechanisms and/or anti-inflammatory commensal bacteria. Thus, the levels of anti-inflammatory commensal bacteria in resident populations may be critical in maintaining this homeostatic balance.Hypothesis/Gap Statement. The incidence of immunosuppressive streptococci in the oral cavity is not well established. Determining the proportion of these organisms and the mechanisms involved may help to understand host-microbe homeostasis and inform development of probiotics or prebiotics in the maintenance of oral health.Aim. To determine the incidence and potential modes of action of immunosuppressive capacity in resident oral streptococci.Methodology. Supragingival plaque was collected from five healthy participants and supragingival and subgingival plaque from five with gingivitis. Twenty streptococci from each sample were co-cultured with epithelial cells±flagellin or LL-37. CXCL8 secretion was detected by ELISA, induction of cytotoxicity in human epithelial cells by lactate dehydrogenase release and NFκB-activation using a reporter cell line. Bacterial identification was achieved through partial 16S rRNA gene sequencing and next-generation sequencing.Results. CXCL8 secretion was inhibited by 94/300 isolates. Immunosuppressive isolates were detected in supragingival plaque from healthy (4/5) and gingivitis (4/5) samples, and in 2/5 subgingival (gingivitis) plaque samples. Most were Streptococcus mitis/oralis. Seventeen representative immunosuppressive isolates all inhibited NFκB activation. The immunosuppressive mechanism was strain specific, often mediated by ultra-violet light-labile factors, whilst bacterial viability was essential in certain species.Conclusion. Many streptococci isolated from plaque suppressed epithelial cell CXCL8 secretion, via inhibition of NFκB. This phenomenon may play an important role in oral host-microbe homeostasis.


Asunto(s)
Inmunomodulación , Interleucina-8/metabolismo , Microbiota/inmunología , Boca/microbiología , FN-kappa B/metabolismo , Streptococcus/inmunología , Células A549 , Línea Celular , Células Epiteliales/metabolismo , Encía/microbiología , Gingivitis/microbiología , Humanos , Microbiota/genética , Streptococcus/clasificación , Streptococcus/genética , Streptococcus/aislamiento & purificación
15.
Sci Total Environ ; 770: 145399, 2021 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-33736375

RESUMEN

Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.


Asunto(s)
Estiércol , Microbiota , Animales , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Granjas , Genes Bacterianos , Metagenómica , Microbiota/genética , ARN Ribosómico 16S , Suelo , Microbiología del Suelo
16.
Environ Sci Technol ; 55(8): 4899-4913, 2021 04 20.
Artículo en Inglés | MEDLINE | ID: mdl-33686859

RESUMEN

Besides the ecotoxicological consequences of microplastics and associated chemicals, the association of microbes on plastics has greater environmental implications as microplastics may select for unique microbiome participating in environmentally significant functions. Despite this, the functional potential of the microbiome associated with different types of plastics is understudied. Here, we investigate the interaction between plastic and marine biofilm-forming microorganisms through a whole-genome sequencing approach on four types of microplastics incubated in the marine environment. Taxonomic analysis suggested that the microplastic surfaces exhibit unique microbial profiles and niche partitioning among the substrates. In particular, the abundance of Vibrio alginolyticus and Vibrio campbellii suggested that microplastic pollution may pose a potential risk to the marine food chain and negatively impact aquaculture industries. Microbial genera involved in xenobiotic compound degradation, carbon cycling, and genes associated with the type IV secretion system, conjugal transfer protein TraG, plant-pathogen interaction, CusA/CzcA family heavy metal efflux transfer proteins, and TolC family proteins were significantly enriched on all the substrates, indicating the variety of processes operated by the plastic-microbiome. The present study gives a detailed characterization of the rapidly altering microbial composition and gene pools on plastics and adds new knowledge surrounding the environmental ramifications of marine plastic pollution.


Asunto(s)
Microbiota , Contaminantes Químicos del Agua , Monitoreo del Ambiente , Contaminación Ambiental , Microbiota/genética , Microplásticos , Plásticos , Vibrio , Contaminantes Químicos del Agua/análisis
17.
Medicine (Baltimore) ; 100(13): e25362, 2021 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-33787640

RESUMEN

ABSTRACT: We investigated the vaginal flora diversity of preschool-aged (ie, 4-6-year-old) girls in southwest China.Fourteen preschool-aged girls were enrolled in this study. The statuses and differences in their vaginal flora were evaluated by Gram staining, bacterial culturing, and sequencing analysis.Gram staining and microbial culturing showed that the main vaginal flora of the preschool-aged girls were Gram-negative bacilli, whereas the main vaginal flora of healthy adult controls were large Gram-positive bacilli such as Lactobacillus crispatus. Shannon and Simpson indexes indicated that the bacterial diversity tended to decrease with age. The species abundance heat map showed that the vaginal microecology of the girls differed slightly at different ages but mainly comprised Pseudomonas, Methylobacterium, Sphingomona,s and Escherichia. The functional abundance heat map indicated that the bacterial functions increased with age.The vaginal microecology of preschool-aged girls differs from that of adults. A comprehensive understanding of the vaginal flora diversity of preschool-aged girls will aid in clinically diagnosing vulvovaginitis in preschool-aged girls.


Asunto(s)
Bacterias/aislamiento & purificación , Microbiota/genética , Vagina/microbiología , Vulvovaginitis/diagnóstico , Adulto , Factores de Edad , Bacterias/genética , Estudios de Casos y Controles , Niño , Preescolar , China , ADN Bacteriano/aislamiento & purificación , Femenino , Voluntarios Sanos , Humanos , Tipificación Molecular/métodos , Análisis de Secuencia de ADN , Frotis Vaginal , Vulvovaginitis/microbiología
18.
Microbiome ; 9(1): 73, 2021 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33766138

RESUMEN

In this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology. Video Abstract.


Asunto(s)
Microbiota , Microbiota/genética , Filogenia
19.
Commun Biol ; 4(1): 240, 2021 02 18.
Artículo en Inglés | MEDLINE | ID: mdl-33603076

RESUMEN

SARS-CoV-2 is the cause of COVID-19. It infects multiple organs including the respiratory tract and gut. Dynamic changes of regional microbiomes in infected adults are largely unknown. Here, we performed longitudinal analyses of throat and anal swabs from 35 COVID-19 and 19 healthy adult controls, as well as 10 non-COVID-19 patients with other diseases, by 16 S rRNA gene sequencing. The results showed a partitioning of the patients into 3-4 categories based on microbial community types (I-IV) in both sites. The bacterial diversity was lower in COVID-19 patients than healthy controls and decreased gradually from community type I to III/IV. Although the dynamic change of microbiome was complex during COVID-19, a synchronous restoration of both the upper respiratory and gut microbiomes from early dysbiosis towards late more diverse status was observed in 6/8 mild COVID-19 adult patients. These findings reveal previously unknown interactions between upper respiratory and gut microbiomes during COVID-19.


Asunto(s)
/microbiología , Microbioma Gastrointestinal , Microbiota , Sistema Respiratorio/microbiología , Adolescente , Adulto , Anciano , Femenino , Microbioma Gastrointestinal/genética , Humanos , Masculino , Microbiota/genética , Persona de Mediana Edad , ARN Ribosómico 16S/genética , Adulto Joven
20.
Environ Toxicol Pharmacol ; 83: 103606, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33545380

RESUMEN

Heavy metal contamination of soil has become a public concern. Earthworms are key players in the functioning and service of soil ecosystems, with comprehension of their introduction in the polluted soil offering new insights into the protection of soil resources. In the present study, we evaluated the effects of earthworm (Eisenia fetida) introduction and Cd (0, 10, 30, and 60 mg kg-1 of Cd) exposure upon soil microbial community using 16S rRNA gene amplicon sequencing. Our research demonstrated that Gemmatimonadetes and Deinococcus-Thermus upregulated significantly, while Chryseolinea showed an obvious decreasing trend after earthworm introduction. In Cd contaminated soil, many genera exhibited a greater presence of Cd-dependent bacteria, namely Cd-tolerant bacteria such as Altererythrobacter and Luteimonas, and a decrease of sensitive bacteria, such as Amaricoccus and Haliangium. Moreover, functional prediction analysis of soil microbiota indicated that earthworm introduction and Cd exposure changed functional pathways of soil microorganisms. The results obtained in this study are beneficial for understanding soil microbial community impacted by earthworm, and for exploring Cd resistant or tolerant bacteria, with potentially significant findings for soil biodiversity and Cd bioremediation.


Asunto(s)
Cadmio/toxicidad , Microbiota/efectos de los fármacos , Oligoquetos , Contaminantes del Suelo/toxicidad , Animales , Bacterias/efectos de los fármacos , Bacterias/genética , Microbiota/genética , ARN Ribosómico 16S , Microbiología del Suelo
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