RESUMEN
Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow to understand the impact of plasmids on the gut microbiome. We create a plasmid phylogenetic tree, devise a method for assigning plasmid hosts, and examine potential plasmid transfer networks. Our research discovers a wide variety of previously unidentified plasmid sequences, indicating that current databases do not fully represent the gut plasmidome. Interestingly, infants display greater plasmid diversity compared to mothers and other healthy adults. We find that Bacteroidota, a major bacterial phylum, serves as the primary host for gut plasmids and plays a dominant role in gut plasmid transfer events. Additionally, plasmids broaden the genetic capabilities of bacteria, with their influence on bacterial function becoming more apparent as children's gut microbiomes develop. This study sheds light on the role of plasmids in the infant gut microbiome, making a significant contribution to our understanding of plasmid biology.
Asunto(s)
Microbioma Gastrointestinal , Filogenia , Plásmidos , Plásmidos/genética , Humanos , Microbioma Gastrointestinal/genética , Lactante , Femenino , Adulto , Bacterias/genética , Bacterias/clasificación , Masculino , Heces/microbiología , Bacteroidetes/genética , Recién NacidoRESUMEN
Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.
Asunto(s)
Metagenoma , Metagenómica , Microbiota , Filogenia , Metagenómica/métodos , Metagenoma/genética , Humanos , Microbiota/genética , Programas Informáticos , Bacterias/genética , Bacterias/clasificación , Genoma Bacteriano/genéticaRESUMEN
BACKGROUND: In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age. RESULTS: We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs. CONCLUSIONS: We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract.
Asunto(s)
Antibacterianos , Bacterias , Microbioma Gastrointestinal , Microbioma Gastrointestinal/genética , Microbioma Gastrointestinal/efectos de los fármacos , Humanos , Lactante , Antibacterianos/farmacología , Bacterias/genética , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Dinamarca , Farmacorresistencia Bacteriana/genética , Genes Bacterianos/genética , Femenino , Heces/microbiología , Farmacorresistencia Microbiana/genética , Masculino , Estudios de Cohortes , Recién NacidoRESUMEN
Plasmid-encoded type IV-A CRISPR-Cas systems lack an acquisition module, feature a DinG helicase instead of a nuclease, and form ribonucleoprotein complexes of unknown biological functions. Type IV-A3 systems are carried by conjugative plasmids that often harbor antibiotic-resistance genes and their CRISPR array contents suggest a role in mediating inter-plasmid conflicts, but this function remains unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 system co-opts the type I-E adaptation machinery from its host, Klebsiella pneumoniae (K. pneumoniae), to update its CRISPR array. Furthermore, we reveal that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By silencing plasmid core functions, type IV-A3 impacts the horizontal transfer and stability of targeted plasmids, supporting its role in plasmid competition. Our findings shed light on the mechanisms and ecological function of type IV-A3 systems and demonstrate their practical efficacy for countering antibiotic resistance in clinically relevant strains.
Asunto(s)
Sistemas CRISPR-Cas , Conjugación Genética , Klebsiella pneumoniae , Plásmidos , Plásmidos/genética , Klebsiella pneumoniae/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Transferencia de Gen Horizontal , Bacteriófagos/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismoRESUMEN
Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within biofilm communities established on plant roots. Here, a well-established four-species biofilm model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, and Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis roots to study the impact of multispecies biofilm on plant growth and the community spatial dynamics on the roots. SPMX co-culture notably promoted root development and plant biomass. Co-cultured SPMX increased root colonization and formed multispecies biofilms, structurally different from those formed by monocultures. By combining 16S rRNA gene amplicon sequencing and fluorescence in situ hybridization with confocal laser scanning microscopy, we found that the composition and spatial organization of the four-species biofilm significantly changed over time. Monoculture P. amylolyticus colonized plant roots poorly, but its population and root colonization were highly enhanced when residing in the four-species biofilm. Exclusion of P. amylolyticus from the community reduced overall biofilm production and root colonization of the three species, resulting in the loss of the plant growth-promoting effects. Combined with spatial analysis, this led to identification of P. amylolyticus as a keystone species. Our findings highlight that weak root colonizers may benefit from mutualistic interactions in complex communities and hereby become important keystone species impacting community spatial organization and function. This work expands the knowledge on spatial organization uncovering interspecific interactions in multispecies biofilm communities on plant roots, beneficial for harnessing microbial mutualism promoting plant growth.
Asunto(s)
Biopelículas , Interacciones Microbianas , Hibridación Fluorescente in Situ , ARN Ribosómico 16S/genética , SimbiosisRESUMEN
Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.
Asunto(s)
Antibacterianos , Microbioma Gastrointestinal , Lactante , Adulto Joven , Humanos , Antibacterianos/farmacología , Microbioma Gastrointestinal/genética , Escherichia coli/genética , Bacterias/genética , Farmacorresistencia Microbiana/genética , Genes BacterianosRESUMEN
INTRODUCTION: Rural children have a lower risk of asthma and atopic diseases than urban children. However, whether indoor microbiota in non-farming rural homes provides protection is unclear. METHODS: Here, we examine if microbes in the beds of rural and urban infants are associated with later development of atopic diseases. We studied fungi and bacteria in the beds of 6-month-old infants (n = 514) in association with the risk of asthma, allergic rhinitis, eczema and aeroallergen sensitization at 6 years of age in the prospective COPSAC2010 cohort. RESULTS: Both fungal and bacterial diversity were lower in the beds of children, who later developed allergic rhinitis (-0.22 [-0.43,-0.01], padj = .04 and -.24 [-0.42,-0.05], padj = .01 respectively) and lower bacterial richness was discovered in beds of children later developing asthma (-41.34 [-76.95,-5.73], padj = .02) or allergic rhinitis (-45.65 [-81.19,-10.10], padj = .01). Interestingly, higher fungal diversity and richness were discovered in the beds of children developing eczema (0.23 [0.02,0.43], padj = .03 and 29.21 [1.59,56.83], padj = .04 respectively). We defined a limited set of fungal and bacterial genera that predicted rural/urban environment. Some rural-associated bacterial genera such as Romboutsia and Bacillus and fungal genera Spegazzinia and Physcia were also associated with reduced risk of diseases, including eczema. These fungal and bacterial fingerprints predicting the living environment were associated with asthma and allergic rhinitis, but not eczema, with rural compositions being protective. The bed dust bacteria mediated 27% of the protective association of a rural living environment for allergic rhinitis (p = .04). CONCLUSIONS: Bed dust microbes can be differentially associated with airway- and skin-related diseases. The differing bed dust microbiota between rural and urban infants may influence their later risk of asthma and allergic rhinitis.
Asunto(s)
Asma , Eccema , Rinitis Alérgica , Lactante , Niño , Humanos , Estudios Prospectivos , Asma/epidemiología , Asma/etiología , Polvo , Bacterias , Rinitis Alérgica/epidemiología , Rinitis Alérgica/etiología , HongosRESUMEN
Many bacteria use CRISPR-Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids1. In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity2,3. Here we unveil a distinct type of CRISPR-Cas Inhibition strategy that is based on small non-coding RNA anti-CRISPRs (Racrs). Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units4. We show that a prophage-encoded Racr strongly inhibits the type I-F CRISPR-Cas system by interacting specifically with Cas6f and Cas7f, resulting in the formation of an aberrant Cas subcomplex. We identified Racr candidates for almost all CRISPR-Cas types encoded by a diverse range of viruses and plasmids, often in the genetic context of other anti-CRISPR genes5. Functional testing of nine candidates spanning the two CRISPR-Cas classes confirmed their strong immune inhibitory function. Our results demonstrate that molecular mimicry of CRISPR repeats is a widespread anti-CRISPR strategy, which opens the door to potential biotechnological applications6.
Asunto(s)
Bacterias , Bacteriófagos , Sistemas CRISPR-Cas , Imitación Molecular , ARN Viral , Bacterias/genética , Bacterias/inmunología , Bacterias/virología , Bacteriófagos/genética , Bacteriófagos/inmunología , Biotecnología/métodos , Biotecnología/tendencias , Proteínas Asociadas a CRISPR/metabolismo , Sistemas CRISPR-Cas/genética , Sistemas CRISPR-Cas/inmunología , Plásmidos/genética , Profagos/genética , Profagos/inmunología , ARN Viral/genéticaRESUMEN
BACKGROUND: Growing up with siblings has been linked to numerous health outcomes and is also an important determinant for the developing microbiota. Nonetheless, research into the role of having siblings on the developing microbiota has mainly been incidental. RESULTS: Here, we investigate the specific effects of having siblings on the developing airway and gut microbiota using a total of 4497 hypopharyngeal and fecal samples taken from 686 children in the COPSAC2010 cohort, starting at 1 week of age and continuing until 6 years of age. Sibship was evaluated longitudinally and used for stratification. Microbiota composition was assessed using 16S rRNA gene amplicon sequencing of the variable V4 region. We found siblings in the home to be one of the most important determinants of the developing microbiota in both the airway and gut, with significant differences in alpha diversity, beta diversity, and relative abundances of the most abundant taxa, with the specific associations being particularly apparent during the first year of life. The age gap to the closest older sibling was more important than the number of older siblings. The signature of having siblings in the gut microbiota at 1 year was associated with protection against asthma at 6 years of age, while no associations were found for allergy. CONCLUSIONS: Having siblings is one of the most important factors influencing a child's developing microbiota, and the specific effects may explain previously established associations between siblings and asthma and infectious diseases. As such, siblings should be considered in all studies involving the developing microbiota, with emphasis on the age gap to the closest older sibling rather than the number of siblings. Video abstract.
Asunto(s)
Asma , Microbioma Gastrointestinal , Microbiota , Niño , Heces , Microbioma Gastrointestinal/genética , Humanos , Microbiota/genética , ARN Ribosómico 16S/genética , HermanosRESUMEN
The majority of ecological, industrial and medical impacts of bacteria result from diverse communities containing multiple species. This diversity presents a significant challenge as co-cultivation of multiple bacterial species frequently leads to species being outcompeted and, with this, the possibility to manipulate, evolve and improve bacterial communities is lost. Ecological theory predicts that a solution to this problem will be to grow species in structured environments, which reduces the likelihood of competitive exclusion. Here, we explored the ability of cultivation in a structured environment to facilitate coexistence, evolution, and adaptation in an industrially important community: Lactococcus lactis and Leuconostoc mesenteroides frequently used as dairy starter cultures. As commonly occurs, passaging of these two species together in a liquid culture model led to the loss of one species in 6 of 20 lineages (30%). By contrast, when we co-cultured the two species as biofilms on beads, a stable coexistence was observed in all lineages studied for over 100 generations. Moreover, we show that the co-culture drove evolution of new high-yield variants, which compared to the ancestor grew more slowly, yielded more cells and had enhanced capability of biofilm formation. Importantly, we also show that these high-yield biofilm strains did not evolve when each species was passaged in monoculture in the biofilm model. Therefore, both co-culture and the biofilm model were conditional for these high-yield strains to evolve. Our study underlines the power of ecological thinking-namely, the importance of structured environments for coexistence-to facilitate cultivation, evolution, and adaptation of industrially important bacterial communities.
Asunto(s)
Biopelículas , Lactococcus lactis , Bacterias , Lactococcus lactis/genéticaRESUMEN
Horizontal gene transfer via plasmids is important for the dissemination of antibiotic resistance genes among medically relevant pathogens. Specifically, the transfer of IncHI1A plasmids is believed to facilitate the spread of antibiotic resistance genes, such as carbapenemases, within the clinically important family Enterobacteriaceae. The microbial community of urban wastewater treatment plants has been shown to be highly permissive towards conjugal transfer of IncP1 plasmids. Here, we tracked the transfer of the P1 plasmid pB10 and the clinically relevant HI1A plasmid R27 in the microbial communities present in urban residential sewage entering full-scale wastewater treatment plants. We found that both plasmids readily transferred to these communities and that strains in the sewage were able to further disseminate them. Furthermore, R27 has a broad potential host range, but a low host divergence. Interestingly, although the majority of R27 transfer events were to members of Enterobacteriaceae, we found a subset of transfer events to other families, even other phyla. This indicates that HI1A plasmids facilitate horizontal gene transfer both within Enterobacteriaceae, but also across families of, in particular, Gammaproteobacteria, such as Moraxellaceae, Pseudomonadaceae and Shewanellaceae. pB10 displayed a similar potential host range to R27. In contrast to R27, pB10 had a high host divergence. By culture enrichment of the transconjugant communities, we show that sewage strains of Enterobacteriaceae and Aeromonadaceae can stably maintain R27 and pB10, respectively. Our results suggest that dissemination in the urban residual water system of HI1A plasmids may result in an accelerated acquisition of antibiotic resistance genes among pathogens.
Asunto(s)
Microbiota , Aguas del Alcantarillado , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Transferencia de Gen Horizontal/genética , Plásmidos/genética , Aguas del Alcantarillado/microbiologíaRESUMEN
Community assembly processes determine patterns of species distribution and abundance which are central to the ecology of microbiomes. When studying plant root microbiome assembly, it is typical to sample at the whole plant root system scale. However, sampling at these relatively large spatial scales may hinder the observability of intermediate processes. To study the relative importance of these processes, we employed millimetre-scale sampling of the cell elongation zone of individual roots. Both the rhizosphere and rhizoplane microbiomes were examined in fibrous and taproot model systems, represented by wheat and faba bean, respectively. Like others, we found that the plant root microbiome assembly is mainly driven by plant selection. However, based on variability between replicate millimetre-scale samples and comparisons with randomized null models, we infer that either priority effects during early root colonization or variable selection among replicate plant roots also determines root microbiome assembly.
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Microbiota , Microbiología del Suelo , Bacterias/genética , Raíces de Plantas , RizosferaRESUMEN
Many prokaryotes encode CRISPR-Cas systems as immune protection against mobile genetic elements (MGEs), yet a number of MGEs also harbor CRISPR-Cas components. With a few exceptions, CRISPR-Cas loci encoded on MGEs are uncharted and a comprehensive analysis of their distribution, prevalence, diversity, and function is lacking. Here, we systematically investigated CRISPR-Cas loci across the largest curated collection of natural bacterial and archaeal plasmids. CRISPR-Cas loci are widely but heterogeneously distributed across plasmids and, in comparison to host chromosomes, their mean prevalence per Mbp is higher and their distribution is distinct. Furthermore, the spacer content of plasmid CRISPRs exhibits a strong targeting bias towards other plasmids, while chromosomal arrays are enriched with virus-targeting spacers. These contrasting targeting preferences highlight the genetic independence of plasmids and suggest a major role for mediating plasmid-plasmid conflicts. Altogether, CRISPR-Cas are frequent accessory components of many plasmids, which is an overlooked phenomenon that possibly facilitates their dissemination across microbiomes.
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Archaea , Sistemas CRISPR-Cas , Archaea/genética , Bacterias/genética , Plásmidos/genética , Células ProcariotasRESUMEN
Biological rapid sand filtration is a commonly employed method for the removal of organic and inorganic impurities in water which relies on the degradative properties of microorganisms for the removal of diverse contaminants, but their bioremediation capabilities vary greatly across waterworks. Bioaugmentation efforts with degradation-proficient bacteria have proven difficult due to the inability of the exogenous microbes to stably colonize the sand filters. Plasmids are extrachromosomal DNA elements that can often transfer between bacteria and facilitate the flow of genetic information across microbiomes, yet their ability to spread within rapid sand filters has remained unknown. Here, we examine the permissiveness of rapid sand filter communities toward four environmentally transmissible plasmids, RP4, RSF1010, pKJK5, and TOL (pWWO), using a dual-fluorescence bioreporter platform combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Our results reveal that plasmids can transfer at high frequencies and across distantly related taxa from rapid sand filter communities, emphasizing their potential suitability for introducing bioremediation determinants in the microbiomes of underperforming water purification plants. IMPORTANCE The supply of clean water for human consumption is being challenged by the appearance of anthropogenic pollutants in groundwater ecosystems. Because many plasmids can transfer horizontally between members of bacterial communities, they comprise promising vectors for the dissemination of pollutant-degrading genetic determinants within water purification plants. However, their ability to spread within groundwater-fed rapid sand filters has not been explored. Here, we investigate the transfer dynamics of four transmissible plasmids across rapid sand filter communities originating from three different waterworks in Denmark. Our results revealed a significant ability of natural plasmids to transfer at high frequencies and across distantly related taxa in the absence of plasmid selection, indicating their potential suitability as vectors for the spread of bioremediation determinants in water purification plants. Future work is required to assess the biotechnological applicability and long-term maintenance of exogenous plasmids within sand filter communities.
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Bacterias/genética , Transferencia de Gen Horizontal , Agua Subterránea/microbiología , Microbiota , Plásmidos/genética , Bacterias/clasificación , Bacterias/aislamiento & purificación , Filtración , Humanos , Filogenia , Dióxido de Silicio/químicaRESUMEN
Plasmids facilitate rapid bacterial adaptation by shuttling a wide variety of beneficial traits across microbial communities. However, under non-selective conditions, maintaining a plasmid can be costly to the host cell. Nonetheless, plasmids are ubiquitous in nature where bacteria adopt their dominant mode of life - biofilms. Here, we demonstrate that biofilms can act as spatiotemporal reserves for plasmids, allowing them to persist even under non-selective conditions. However, under these conditions, spatial stratification of plasmid-carrying cells may promote the dispersal of cells without plasmids, and biofilms may thus act as plasmid sinks.
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Biopelículas , Microbiota , Adaptación Fisiológica , Bacterias/genética , Plásmidos/genéticaRESUMEN
Antimicrobial resistance (AMR) is an accelerating global threat, yet the nature of AMR in the gut microbiome and how AMR is acquired during early life remain largely unknown. In a cohort of 662 Danish children, we characterized the antibiotic resistance genes (ARGs) acquired during the first year of life and assessed the impacts of diverse environmental exposures on ARG load. Our study reveals a clear bimodal distribution of ARG richness that is driven by the composition of the gut microbiome, especially E. coli. ARG profiles were significantly affected by various environmental factors. Among these factors, the importance of antibiotics diminished with time since treatment. Finally, ARG load and ARG clusters were also associated with the maturity of the gut microbiome and a bacterial composition associated with increased risk of asthma. These findings broaden our understanding of AMR in early life and have critical implications for efforts to mitigate its spread.
Asunto(s)
Antibacterianos/farmacología , Asma/microbiología , Farmacorresistencia Microbiana/genética , Exposición a Riesgos Ambientales/estadística & datos numéricos , Escherichia coli/genética , Microbioma Gastrointestinal/efectos de los fármacos , Niño , Preescolar , Estudios de Cohortes , ADN Bacteriano , Escherichia coli/efectos de los fármacos , Heces/microbiología , Femenino , Genes Bacterianos , Humanos , Lactante , Recién Nacido , Masculino , Metagenómica , Embarazo , Proteobacteria/efectos de los fármacos , Medición de RiesgoRESUMEN
Automated classification of CRISPR-Cas systems has been challenged by their dynamic nature and expanding classification. Here, we developed CRISPRCasTyper, an automated tool with improved capabilities for identifying and typing CRISPR arrays and cas loci based on the latest nomenclature (44 subtypes/variants). As a novel feature, CRISPRCasTyper uses a machine learning approach to subtype CRISPR arrays based on the sequences of the repeats, which allows the typing of orphan and distant arrays. CRISPRCasTyper provides a graphical output, where CRISPRs and cas operons are visualized as gene maps, thus aiding annotation of partial and novel systems through synteny. CRISPRCasTyper was benchmarked against a manually curated set of 31 subtypes with a median accuracy of 98.6% and used to explore CRISPR-Cas diversity across >3,000 metagenomes. Altogether, we present an up-to-date software for improved automated prediction of CRISPR-Cas loci. CRISPRCasTyper is available through conda and as a web server (cctyper.crispr.dk).
Asunto(s)
Sistemas CRISPR-Cas/genética , Edición Génica/clasificación , Edición Génica/métodos , Archaea/genética , Proteína 9 Asociada a CRISPR/genética , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas/genética , Edición Génica/tendencias , Genoma Bacteriano/genética , Metagenoma/genética , Filogenia , ARN Guía de Kinetoplastida/genética , Programas InformáticosRESUMEN
BACKGROUND: From early life, children are exposed to a multitude of environmental exposures, which may be of crucial importance for healthy development. Here, the environmental microbiota may be of particular interest as it represents the interface between environmental factors and the child. As infants in modern societies spend a considerable amount of time indoors, we hypothesize that the indoor bed dust microbiota might be an important factor for the child and for the early colonization of the airway microbiome. To explore this hypothesis, we analyzed the influence of environmental exposures on 577 dust samples from the beds of infants together with 542 airway samples from the Copenhagen Prospective Studies on Asthma in Childhood2010 cohort. RESULTS: Both bacterial and fungal community was profiled from the bed dust. Bacterial and fungal diversity in the bed dust was positively correlated with each other. Bacterial bed dust microbiota was influenced by multiple environmental factors, such as type of home (house or apartment), living environment (rural or urban), sex of siblings, and presence of pets (cat and/or dog), whereas fungal bed dust microbiota was majorly influenced by the type of home (house or apartment) and sampling season. We further observed minor correlation between bed dust and airway microbiota compositions among infants. We also analyzed the transfer of microbiota from bed dust to the airway, but we did not find evidence of transfer of individual taxa. CONCLUSIONS: Current study explores the influence of environmental factors on bed dust microbiota (both bacterial and fungal) and its correlation with airway microbiota (bacterial) in early life using high-throughput sequencing. Our findings demonstrate that bed dust microbiota is influenced by multiple environmental exposures and could represent an interface between environment and child. Video Abstract.
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Bacterias/aislamiento & purificación , Lechos/microbiología , Polvo , Ambiente , Hongos/aislamiento & purificación , Micobioma , Sistema Respiratorio/microbiología , Animales , Bacterias/genética , Gatos , Dinamarca , Perros , Femenino , Hongos/genética , Vivienda , Humanos , Lactante , Masculino , Micobioma/genética , Mascotas/microbiología , Estudios Prospectivos , Salud Rural , Estaciones del Año , Hermanos , Salud UrbanaRESUMEN
Activity of the microbial population in clothing causes unpleasant odor and textile deterioration. However, little is known about how the textile microbial community is shaped. In this study, we developed a method for extracting DNA from small amounts of detergent-washed clothing, and applied it to both worn and unworn, washed and unwashed cotton and polyester samples of the axillary region of T-shirts from 10 male subjects. The combined application of 16S rRNA gene amplicon sequencing and quantitative PCR allowed us to estimate the absolute abundances of bacteria in the samples. We found that the T-shirt microbiome was highly individual, both in composition, diversity and microbial biomass. Fabric type was influential where Acinetobacter was more abundant in cotton. Intriguingly, unworn cotton T-shirts had a native microbiome dominated by Acinetobacter, whereas unworn polyester had no detectable bacterial microbiome. The native textile microbiome did not seem to have any effect on the microbial composition emerging from wearing the garment. Surprisingly, washing in mild detergent had only minor effects on the composition and biomass of the microbial community, and only few Amplicon Sequence Variants (ASV)s were found to decrease in abundance after washing. Individual variations between test subjects shaped the microbial community more than the type of fabric or wash with detergent. The individuality of T-shirt microbiomes and specificity of the washing procedure suggests that personalized laundry regimes could be applied to increase efficient removal of undesired bacteria.
Asunto(s)
Microbiota , Bacterias/genética , ADN , Humanos , Masculino , ARN Ribosómico 16S/genética , TextilesRESUMEN
CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites. In contrast to all other types of CRISPR-Cas systems, type IV has remained largely overlooked. Here, we describe a previously uncharted diversity of type IV gene cassettes, primarily encoded by plasmid-like elements from diverse prokaryotic taxa. Remarkably, via a comprehensive analysis of their CRISPR spacer content, these systems were found to exhibit a strong bias towards the targeting of other plasmids. Our data indicate that the functions of type IV systems have diverged from those of other host-related CRISPR-Cas immune systems to adopt a role in mediating conflicts between plasmids. Furthermore, we find evidence for cross-talk between certain type IV and type I CRISPR-Cas systems that co-exist intracellularly, thus providing a simple answer to the enigmatic absence of type IV adaptation modules. Collectively, our results lead to the expansion and reclassification of type IV systems and provide novel insights into the biological function and evolution of these elusive systems.