Publications by authors named "Søren J Sørensen"

194 Publications

Comparative Genomics Analysis of Keratin-Degrading Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production.

Microorganisms 2021 May 12;9(5). Epub 2021 May 12.

Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.

A promising keratin-degrading strain from the genus ( sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic species and shades lights on the keratinolytic potential of sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.
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http://dx.doi.org/10.3390/microorganisms9051042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8151938PMC
May 2021

Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage.

Environ Sci Technol 2021 05 22;55(9):5939-5949. Epub 2021 Apr 22.

Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK.

Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum β-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (10-10 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (10-10 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum β-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.
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http://dx.doi.org/10.1021/acs.est.0c08548DOI Listing
May 2021

Temporal oral microbiome changes with brushing in children with cleft lip and palate.

Heliyon 2021 Mar 18;7(3):e06513. Epub 2021 Mar 18.

University of Coimbra, Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.

This cohort study aimed to characterize the oral microbiome of children with CLP, from two different age groups, and evaluate the effect of supervised or unsupervised toothbrushing on the microbiome of the cleft over time. Swab samples were collected from the cleft area at three different time points (A; no brushing, B; after 15 days and C; after 30 days) and were analyzed using next-generation sequencing to determine the microbial composition and diversity in these time points. Overall, brushing significantly decreased the abundance of the genera and in the two age groups examined, and for this decrease was more evident for children (2-6 years old). In the preteen group (7-12 years old), a significant relative increase of the genus was observed after brushing. In this study, the systematic brushing over a period of thirty days also resulted in differences at the intra-individual bacterial richness.
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http://dx.doi.org/10.1016/j.heliyon.2021.e06513DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8005767PMC
March 2021

Comparative analysis of the alveolar microbiome in COPD, ECOPD, Sarcoidosis, and ILD patients to identify respiratory illnesses specific microbial signatures.

Sci Rep 2021 Feb 17;11(1):3963. Epub 2021 Feb 17.

Department of Biochemistry, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.

Studying respiratory illness-specific microbial signatures and their interaction with other micro-residents could provide a better understanding of lung microbial ecology. Each respiratory illness has a specific disease etiology, however, so far no study has revealed disease-specific microbial markers. The present study was designed to determine disease-specific microbial features and their interactions with other residents in chronic obstructive pulmonary diseases (stable and exacerbated), sarcoidosis, and interstitial lung diseases. Broncho-alveolar lavage samples (n = 43) were analyzed by SSU rRNA gene sequencing to study the alveolar microbiome in these diseases. A predominance of Proteobacteria followed by Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria was observed in all the disease subsets. Shannon diversity was significantly higher in stable COPD when compared to exacerbated chronic obstructive pulmonary disease (ECOPD) (p = 0.0061), and ILD patient samples (p = 0.037). The lung microbiome of the patients with stable COPD was more diverse in comparison to ECOPD and ILD patients (p < 0.001). Lefse analysis identified 40 disease-differentiating microbial features (LDA score (log10) > 4). Species network analysis indicated a significant correlation (p < 0.05) of diseases specific microbial signature with other lung microbiome members. The current study strengthens the proposed hypothesis that each respiratory illness has unique microbial signatures. These microbial signatures could be used as diagnostic markers to differentiate among various respiratory illnesses.
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http://dx.doi.org/10.1038/s41598-021-83524-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889618PMC
February 2021

Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis.

FEMS Microbiol Ecol 2021 03;97(4)

Julius Kühn-Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.

A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents to spread in soil. 'M26' apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of operational taxonomic units affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility of the ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.
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http://dx.doi.org/10.1093/femsec/fiab031DOI Listing
March 2021

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories.

FEMS Microbiol Ecol 2021 03;97(4)

Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
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http://dx.doi.org/10.1093/femsec/fiab027DOI Listing
March 2021

Tillage shapes the soil and rhizosphere microbiome of barley-but not its susceptibility towards Blumeria graminis f. sp. hordei.

FEMS Microbiol Ecol 2021 03;97(3)

Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.

Long-term agricultural practices are assumed to shape the rhizosphere microbiome of crops with implications for plant health. In a long-term field experiment, we investigated the effect of different tillage and fertilization practices on soil and barley rhizosphere microbial communities by means of amplicon sequencing of 16S rRNA gene fragments from total community DNA. Differences in the microbial community composition depending on the tillage practice, but not the fertilization intensity were revealed. To examine whether these soil and rhizosphere microbiome differences influence the plant defense response, barley (cultivar Golden Promise) was grown in field or standard potting soil under greenhouse conditions and challenged with Blumeria graminis f. sp. hordei (Bgh). Amplicon sequence analysis showed that preceding tillage practice, but also aboveground Bgh challenge significantly influenced the microbial community composition. Expression of plant defense-related genes PR1b and PR17b was higher in challenged compared to unchallenged plants. The Bgh infection rates were strikingly lower for barley grown in field soil compared to potting soil. Although previous agricultural management shaped the rhizosphere microbiome, no differences in plant health were observed. We propose therefore that the management-independent higher microbial diversity of field soils compared to potting soils contributed to the low infection rates of barley.
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http://dx.doi.org/10.1093/femsec/fiab018DOI Listing
March 2021

Large-scale association analyses identify host factors influencing human gut microbiome composition.

Nat Genet 2021 02 18;53(2):156-165. Epub 2021 Jan 18.

Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.

To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10 < P < 5 × 10) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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http://dx.doi.org/10.1038/s41588-020-00763-1DOI Listing
February 2021

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas.

FEMS Microbiol Ecol 2021 03;97(3)

Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.

Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
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http://dx.doi.org/10.1093/femsec/fiab007DOI Listing
March 2021

Urbanized microbiota in infants, immune constitution, and later risk of atopic diseases.

J Allergy Clin Immunol 2020 Dec 15. Epub 2020 Dec 15.

Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Gentofte, Denmark.

Background: Urbanization is linked with an increased burden of asthma and atopic traits. A putative mechanism is insufficient exposure to beneficial microbes early in life, leading to immune dysregulation, as was previously shown for indoor microbial exposures.

Objective: Our aim was to investigate whether urbanization is associated with the microbiota composition in the infants' body and early immune function, and whether these contribute to the later risk of asthma and atopic traits.

Methods: We studied the prospective Copenhagen Prospective Studies on Asthma in Childhood 2010 mother-child cohort of 700 children growing up in areas with different degrees of urbanization. During their first year of life, airway and gut microbiotas, as well as immune marker concentrations, were defined. When the children were 6 years of age, asthma and atopic traits were diagnosed by pediatricians.

Results: In adjusted analyses, the risk of asthma and aeroallergen sensitization were increased in urban infants. The composition of especially airway but also gut microbiotas differed between urban and rural infants. The living environment-related structure of the airway microbiota was already associated with immune mediator concentrations at 1 month of age. An urbanized structure of the airway and gut microbiotas was associated with an increased risk of asthma coherently during multiple time points and also with the risks of eczema and sensitization.

Conclusion: Our findings suggest that urbanization-related changes in the infant microbiota may elevate the risk of asthma and atopic traits, probably via cross talk with the developing immune system. The airways may facilitate this effect, as they are open for colonization by environmental airborne microbes and serve as an immune interface.
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http://dx.doi.org/10.1016/j.jaci.2020.12.621DOI Listing
December 2020

CRISPRCasTyper: Automated Identification, Annotation, and Classification of CRISPR-Cas Loci.

CRISPR J 2020 12 4;3(6):462-469. Epub 2020 Dec 4.

Section of Microbiology, University of Copenhagen, Copenhagen, Denmark; Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.

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 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 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).
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http://dx.doi.org/10.1089/crispr.2020.0059DOI Listing
December 2020

Persistence and progression of staphylococcal infection in the presence of public goods.

NPJ Biofilms Microbiomes 2020 11 27;6(1):55. Epub 2020 Nov 27.

Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100, Copenhagen, Denmark.

Staphylococcus aureus is a prominent etiological agent of suppurative abscesses. In principle, abscess formation and purulent exudate are classical physiological features of healing and tissue repair. However, S. aureus deploys two coagulases that can usurp this classical host response and form distinct abscess lesions. Here, we establish that during coinfection with coagulase producers and non-producers, coagulases are shared public goods that contribute to staphylococcal persistence, abscess formation, and disease progression. Coagulase-negative mutants that do not produce the public goods themselves are able to exploit those cooperatively secreted by producers and thereby thrive during coinfection at the expense of others. This study shows the importance of social interactions among pathogens concerning clinical outcomes.
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http://dx.doi.org/10.1038/s41522-020-00168-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7699630PMC
November 2020

Metagenomic analysis of a keratin-degrading bacterial consortium provides insight into the keratinolytic mechanisms.

Sci Total Environ 2021 Mar 29;761:143281. Epub 2020 Oct 29.

Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Keratin is an insoluble fibrous protein from natural environments, which can be recycled to value-added products by keratinolytic microorganisms. A microbial consortium with efficient keratinolytic activity was previously enriched from soil, but the genetic basis behind its remarkable degradation properties was not investigated yet. To identify the metabolic pathways involved in keratinolysis and clarify the observed synergy among community members, shotgun metagenomic sequencing was performed to reconstruct metagenome-assembled genomes. More than 90% genera of the enriched bacterial consortium were affiliated to Chryseobacterium, Stenotrophomonas, and Pseudomonas. Metabolic potential and putative keratinases were predicted from the metagenomic annotation, providing the genetic basis of keratin degradation. Furthermore, metabolic pathways associated with keratinolytic processes such as amino acid metabolism, disulfide reduction and urea cycle were investigated from seven high-quality metagenome-assembled genomes, revealing the potential metabolic cooperation related to keratin degradation. This knowledge deepens the understanding of microbial keratinolytic mechanisms at play in a complex community, pinpointing the significance of synergistic interactions, which could be further used to optimize industrial keratin degradation processes.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143281DOI Listing
March 2021

Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma.

Sci Transl Med 2020 11;12(569)

COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark.

There have been reports of associations between cesarean section delivery and the risk of childhood asthma, potentially mediated through changes in the gut microbiota. We followed 700 children in the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) cohort prospectively from birth. We examined the effects of cesarean section delivery on gut microbial composition by 16 rRNA gene amplicon sequencing during the first year of life. We then explored whether gut microbial perturbations due to delivery mode were associated with a risk of developing asthma in the first 6 years of life. Delivery by cesarean section was accompanied by marked changes in gut microbiota composition at one week and one month of age, but by one year of age only minor differences persisted compared to vaginal delivery. Increased asthma risk was found in children born by cesarean section only if their gut microbiota composition at 1 year of age still retained a cesarean section microbial signature, suggesting that appropriate maturation of the gut microbiota could mitigate against the increased asthma risk associated with gut microbial changes due to cesarean section delivery.
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http://dx.doi.org/10.1126/scitranslmed.aax9929DOI Listing
November 2020

Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements.

Nat Commun 2020 11 6;11(1):5652. Epub 2020 Nov 6.

Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.

Many prokaryotes employ CRISPR-Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I-F (Pseudomonas, Pectobacterium, and Serratia), I-E (Pseudomonas and Serratia), and I-C (Pseudomonas). We uncover 11 type I-F and/or I-E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.
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http://dx.doi.org/10.1038/s41467-020-19415-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648647PMC
November 2020

Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design.

FEMS Microbiol Ecol 2020 12;96(12)

University of Copenhagen, Department of Biology, Section of Microbiology, Copenhagen, Denmark.

Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.
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http://dx.doi.org/10.1093/femsec/fiaa211DOI Listing
December 2020

A converging subset of soil bacterial taxa is permissive to the IncP-1 plasmid pKJK5 across a range of soil copper contamination.

FEMS Microbiol Ecol 2020 10;96(11)

Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.

Stressors like metals or antibiotics can affect bacterial community permissiveness for plasmid uptake, but there is little knowledge about long-term effects of such stressors on the evolution of community permissiveness. We assessed the effect of more than 90 years of soil Cu contamination on bacterial community permissiveness (i.e. uptake ability) toward a gfp-tagged IncP-1 plasmid (pKJK5) introduced via an Escherichia coli donor. Plasmid transfer events from the donor to the recipient soil bacterial community were quantified and transconjugants were subsequently isolated by fluorescence activated cell sorting and identified by 16S rRNA gene amplicon sequencing. Transfer frequency of plasmid pKJK5 was reduced in bacterial communities extracted from highly Cu contaminated (4526 mg kg-1) soil compared to corresponding communities extracted from moderately (458 mg kg-1) Cu contaminated soil and a low Cu reference soil (15 mg kg-1). The taxonomic composition of the transconjugal pools showed remarkable similarities irrespective of the degree of soil Cu contamination and despite contrasting compositions of the extracted recipient communities and the original soil communities. Permissiveness assessed at the level of individual operational taxonomic units (OTUs; 16S rRNA gene 97% sequence similarity threshold) was only slightly affected by soil Cu level and high replicate variability of OTU-level permissiveness indicated a role of stochastic events in IncP-1 plasmid transfer or strain-to-strain permissiveness variability.
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http://dx.doi.org/10.1093/femsec/fiaa200DOI Listing
October 2020

The initial inoculation ratio regulates bacterial coculture interactions and metabolic capacity.

ISME J 2021 01 4;15(1):29-40. Epub 2020 Sep 4.

Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark.

Coculture is an important model system in microbial ecology studies. As a key experimental parameter, the initial inoculation ratio has a crucial impact on the results of the coculture system. However, such an effect has never been investigated under multiple niche conditions. In this study, we established a simple coculture system with two model bacteria in various carbon sources and investigated the influence of initial inoculum ratios of 1:1000 to 1000:1 on community structure, function, and bacterial interaction. We found that the final ratio of the cocultures with different initial inoculum ratios differed in approximately five-sixths of the carbon sources, suggesting that the final ratio is highly dependent on the initial inoculum ratio, while the carbon source preferences of bacteria could not predict the final ratio of cocultures. Furthermore, we found that the initial ratio could regulate the metabolic capacity of the coculture, as only cocultures with initial ratios of 1:1 and 1000:1 gained high capacity on 14 specific carbon sources. The underlying reason may be that the pattern of species interaction is changed by the initial ratio. In conclusion, we showed that the initial ratio can induce emergent properties in coculture. These findings suggest that the initial ratio not only impacts the reproducibility of coculture experiments but also can influence our understanding of generic microbial ecology.
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http://dx.doi.org/10.1038/s41396-020-00751-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7852870PMC
January 2021

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota.

Microbiome 2020 08 7;8(1):115. Epub 2020 Aug 7.

Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, bldg. 1, DK2100, Copenhagen, Denmark.

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 Childhood 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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http://dx.doi.org/10.1186/s40168-020-00895-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7414761PMC
August 2020

Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review.

Sci Total Environ 2020 Nov 11;743:140804. Epub 2020 Jul 11.

Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel.

Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded. Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis. Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140804DOI Listing
November 2020

Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age.

J Allergy Clin Immunol 2020 12 18;146(6):1358-1366. Epub 2020 Jul 18.

Departments of Human Genetics, The University of Chicago, Chicago, Ill. Electronic address:

Background: The upper airways present a barrier to inhaled allergens and microbes, which alter immune responses and subsequent risk for diseases, such as allergic rhinitis (AR).

Objective: We tested the hypothesis that early-life microbial exposures leave a lasting signature in DNA methylation that ultimately influences the development of AR in children.

Methods: We studied upper airway microbiota at 1 week, 1 month, and 3 months of life, and measured DNA methylation and gene expression profiles in upper airway mucosal cells and assessed AR at age 6 years in children in the Copenhagen Prospective Studies on Asthma in Childhood birth cohort.

Results: We identified 956 AR-associated differentially methylated CpGs in upper airway mucosal cells at age 6 years, 792 of which formed 3 modules of correlated differentially methylated CpGs. The eigenvector of 1 module was correlated with the expression of genes enriched for lysosome and bacterial invasion of epithelial cell pathways. Early-life microbial diversity was lower at 1 week (richness P = .0079) in children with AR at age 6 years, and reduced diversity at 1 week was also correlated with the same module's eigenvector (ρ = -0.25; P = 3.3 × 10). We show that the effect of microbiota richness at 1 week on risk for AR at age 6 years was mediated in part by the epigenetic signature of this module.

Conclusions: Our results suggest that upper airway microbial composition in infancy contributes to the development of AR during childhood, and this trajectory is mediated, at least in part, through altered DNA methylation patterns in upper airway mucosal cells.
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http://dx.doi.org/10.1016/j.jaci.2020.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821422PMC
December 2020

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil.

Microorganisms 2020 Jul 9;8(7). Epub 2020 Jul 9.

Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.

Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage ( L. subsp (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of serovar Typhimurium strain 14028s and serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of grown on soil inoculated with . We detected in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens.
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http://dx.doi.org/10.3390/microorganisms8071020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409118PMC
July 2020

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes.

FEMS Microbiol Ecol 2020 06;96(6)

Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.

Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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http://dx.doi.org/10.1093/femsec/fiaa076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781699PMC
June 2020

Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms.

Environ Microbiol 2020 07 12;22(7):2639-2652. Epub 2020 Mar 12.

Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.

Fresh fruits and vegetables have numerous benefits to human health. Unfortunately, their consumption is increasingly associated with food-borne diseases, Salmonella enterica being their most frequent cause in Europe. Agricultural soils were postulated as reservoir of human pathogens, contributing to the contamination of crops during the growing period. Since the competition with the indigenous soil microbiota for colonization sites plays a major role in the success of invading species, we hypothesized that reduced diversity will enhance the chance of Salmonella to successfully establish in agricultural environments. We demonstrated that the abundance of Salmonella drastically decreased in soil with highly diverse indigenous prokaryotic community, while in soil with reduced prokaryotic diversity, Salmonella persisted for a long period. Furthermore, in communities with low diversity, Salmonella had an impact on the abundance of other taxa. The high physiological plasticity allows Salmonella to use agricultural soils as alternative habitat which might provide a route of animal/human infections. In addition, adjusted transcriptional profile with amino acid biosynthesis and the glyoxylate cycle most prominently regulated, suggests an adaptation to the soil environment. Our results underline the importance of the maintenance of diverse soil microbiome as a part of strategy aiming at reduced risk of food-borne salmonellosis outbreaks.
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http://dx.doi.org/10.1111/1462-2920.14972DOI Listing
July 2020

Azo dying of α-keratin material improves microbial keratinase screening and standardization.

Microb Biotechnol 2020 07 28;13(4):984-996. Epub 2020 Feb 28.

Section of Microbiology, University of Copenhagen, DK-2100, Copenhagen, Denmark.

Microbial conversion through enzymatic reactions has received a lot of attention as a cost-effective and environmentally friendly way to recover amino acids and short peptides from keratin materials. However, accurate assessment of microbial keratinase activity is not straightforward, and current available methods lack sensitivity and standardization. Here, we suggest an optimized Azokeratin assay, with substrate generated directly from azo-dyed raw keratin material. We introduced supernatant filtration in the protocol for optimal stopping of keratinase reactions instead of the widely used trichloroacetic acid (TCA), as it generated biases and impacted the sensitivity. We furthermore suggest a method for standardization of keratinase activity signals using proteinase K, a well-known keratinase, as a reference enabling reproducibility between studies. Lastly, we evaluated our developed method with several bacterial isolates through benchmarking against a commercial assay (Keratin Azure). Under different setups, the Azokeratin method was more sensitive than commonly used Keratin Azure-based assays (3-fold). We argue that this method could be applied with any type of keratin substrate, enabling more robust and sensitive results which can be used for further comparison with other studies, thus representing an important progress within the field of microbial keratin degradation.
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http://dx.doi.org/10.1111/1751-7915.13541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7264887PMC
July 2020

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes.

ISME J 2020 05 4;14(5):1170-1181. Epub 2020 Feb 4.

Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.
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http://dx.doi.org/10.1038/s41396-020-0596-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7174300PMC
May 2020

Community-intrinsic properties enhance keratin degradation from bacterial consortia.

PLoS One 2020 31;15(1):e0228108. Epub 2020 Jan 31.

Section for Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

Although organic matter may accumulate sometimes (e.g. lignocellulose in peat bog), most natural biodegradation processes are completed until full mineralization. Such transformations are often achieved by the concerted action of communities of interacting microbes, involving different species each performing specific tasks. These interactions can give rise to novel "community-intrinsic" properties, through e.g. activation of so-called "silent genetic pathways" or synergistic interplay between microbial activities and functions. Here we studied the microbial community-based degradation of keratin, a recalcitrant biological material, by four soil isolates, which have previously been shown to display synergistic interactions during biofilm formation; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. We observed enhanced keratin weight loss in cultures with X. retroflexus, both in dual and four-species co-cultures, as compared to expected keratin degradation by X. retroflexus alone. Additional community intrinsic properties included accelerated keratin degradation rates and increased biofilm formation on keratin particles. Comparison of secretome profiles of X. retroflexus mono-cultures to co-cultures revealed that certain proteases (e.g. serine protease S08) were significantly more abundant in mono-cultures, whereas co-cultures had an increased abundance of proteins related to maintaining the redox environment, e.g. glutathione peroxidase. Hence, one of the mechanisms related to the community intrinsic properties, leading to enhanced degradation from co-cultures, might be related to a switch from sulfitolytic to proteolytic functions between mono- and co-cultures, respectively.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228108PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994199PMC
May 2020

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures.

Front Microbiol 2019 10;10:3010. Epub 2020 Jan 10.

Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.
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http://dx.doi.org/10.3389/fmicb.2019.03010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6968696PMC
January 2020

Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and .

Front Microbiol 2019 10;10:2835. Epub 2020 Jan 10.

Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.

(biovar2, race3) is the causal agent of bacterial wilt and this quarantine phytopathogen is responsible for massive losses in several commercially important crops. Biological control of this pathogen might become a suitable plant protection measure in areas where is endemic. Two bacterial strains, (B63) and (P142) with antagonistic activity toward (B3B) were tested for rhizosphere competence, efficient biological control of wilt symptoms on greenhouse-grown tomato, and effects on the indigenous rhizosphere prokaryotic communities. The population densities of B3B and the antagonists were estimated in rhizosphere community DNA by selective plating, real-time quantitative PCR, and -specific PCR-Southern blot hybridization. Moreover, we investigated how the pathogen and/or the antagonists altered the composition of the tomato rhizosphere prokaryotic community by 16S rRNA gene amplicon sequencing. (B63) and (P142)-inoculated plants showed drastically reduced wilt disease symptoms, accompanied by significantly lower abundance of the B3B population compared to the non-inoculated pathogen control. Pronounced shifts in prokaryotic community compositions were observed in response to the inoculation of B63 or P142 in the presence or absence of the pathogen B3B and numerous dynamic taxa were identified. Confocal laser scanning microscopy (CLSM) visualization of the -tagged antagonist P142 revealed heterogeneous colonization patterns and P142 was detected in lateral roots, root hairs, epidermal cells, and within xylem vessels. Although competitive niche exclusion cannot be excluded, it is more likely that the inoculation of P142 or B63 and the corresponding microbiome shifts primed the plant defense against the pathogen B3B. Both inoculants are promising biological agents for efficient control of under field conditions.
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http://dx.doi.org/10.3389/fmicb.2019.02835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6967407PMC
January 2020

Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial.

Nat Commun 2020 01 22;11(1):426. Epub 2020 Jan 22.

COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2100, Copenhagen, Denmark.

Maternal dietary interventions during pregnancy with fish oil and high dose vitamin D have been shown to reduce the incidence of asthma and wheeze in offspring, potentially through microbial effects in pregnancy or early childhood. Here we analyze the bacterial compositions in longitudinal samples from 695 pregnant women and their children according to intervention group in a nested, factorial, double-blind, placebo-controlled, randomized trial of n-3 long-chain fatty acids and vitamin D supplementation. The dietary interventions affect the infant airways, but not the infant fecal or maternal vaginal microbiota. Changes in overall beta diversity are observed, which in turn associates with a change in immune mediator profile. In addition, airway microbial maturation and the relative abundance of specific bacterial genera are altered. Furthermore, mediation analysis reveals the changed airway microbiota to be a minor and non-significant mediator of the protective effect of the dietary interventions on risk of asthma. Our results demonstrate the potential of prenatal dietary supplements as manipulators of the early airway bacterial colonization.
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http://dx.doi.org/10.1038/s41467-020-14308-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976654PMC
January 2020