scholarly journals Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Francesco Asnicar ◽  
Serena Manara ◽  
Moreno Zolfo ◽  
Duy Tin Truong ◽  
Matthias Scholz ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Community Dynamics ◽  
Common Species ◽  
Strain Level ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Infant Exposure ◽  
Early Infant ◽  
As Species ◽  
Considerable Strain

ABSTRACT Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome. The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.

scholarly journals Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling

2016 ◽  
Author(s):  
Francesco Asnicar ◽  
Serena Manara ◽  
Moreno Zolfo ◽  
Duy Tin Truong ◽  
Matthias Scholz ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Gut Microbiome ◽  
Community Dynamics ◽  
Infant Health ◽  
Common Species ◽  
Strain Level ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomics ◽  
Early Infant

AbstractThe gut microbiome starts to be shaped in the first days of life and continues to increase its diversity during the first months. Several investigations are assessing the link between the configuration of the infant gut microbiome and infant health, but a comprehensive strain-level assessment of vertically transmitted microbes from mother to infant is still missing. We longitudinally collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life, and applied shotgun metagenomic sequencing followed by strain-level profiling. We observed several specific strains including those from Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, that were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo expression of vertically transmitted microbes, for example Bacteroides vulgatus and Bifidobacterium spp., thus suggesting that transmitted strains are functionally active in the two rather different environments of the adult and infant guts. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we showed that it is possible to track vertical transmission of members of the microbiome from mother to infants and characterize their transcriptional activity. Our work poses the basis for surveying at larger scale the sources of microbial diversity in the infants and starts associating these transmissions with the subsequent longer-term development of a healthy or dysbiotic microbiome.ImportanceEarly infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support that the maternal microbial reservoir is a key route of microbial transmission, yet much is inferred from the observation of shared species in mother and infant. Common species, per se, does not necessarily equate vertical transmission as species exhibit considerable strain heterogeneity and it is therefore imperative to identify shared strains. We demonstrate here the potential of shotgun metagenomics and strain-level resolution to identify vertical transmission events via the maternal source. Combined with a metatranscriptomic approach, we show the potential not only to identify and track the fate of microbes in the early infant microbiome but also identify the metabolically active members. These approaches will ultimately provide important insights into the acquisition, development and community dynamics of the infant microbiome.

scholarly journals Exploring Vertical Transmission of Bifidobacteria from Mother to Child

2015 ◽  
Vol 81 (20) ◽  
pp. 7078-7087 ◽  
Author(s):  
Christian Milani ◽  
Leonardo Mancabelli ◽  
Gabriele Andrea Lugli ◽  
Sabrina Duranti ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Bifidobacterium Longum ◽  
Microbial Colonization ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Birth Canal ◽  
Strain Isolation ◽  
Mother And Child ◽  
Metagenomics Data ◽  
Microbiome Data

ABSTRACTPassage through the birth canal and consequent exposure to the mother's microbiota is considered to represent the initiating event for microbial colonization of the gastrointestinal tract of the newborn. However, a precise evaluation of such suspected vertical microbiota transmission has yet to be performed. Here, we evaluated the microbiomes of four sample sets, each consisting of a mother's fecal and milk samples and the corresponding infant's fecal sample, by means of amplicon-based profiling supported by shotgun metagenomics data for two key samples. Notably, targeted genome reconstruction from microbiome data revealed vertical transmission of aBifidobacterium brevestrain and aBifidobacterium longumsubsp.longumstrain from mother to infant, a notion confirmed by strain isolation and genome sequencing. Furthermore, PCR analyses targeting unique genes from these two strains highlighted their persistence in the infant gut at 6 months. Thus, this study demonstrates the existence of specific bifidobacterial strains that are common to mother and child and thus indicative of vertical transmission and that are maintained in the infant for at least relatively short time spans.

scholarly journals Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak

2021 ◽  
Vol 7 (4) ◽  
Author(s):  
Florence E. Buytaers ◽  
Assia Saltykova ◽  
Wesley Mattheus ◽  
Bavo Verhaegen ◽  
Nancy H. C. Roosens ◽  
...  
Keyword(s):  
Food Samples ◽  
Strain Level ◽  
Outbreak Investigation ◽  
Reference Laboratory ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
National Reference ◽  
Link Type ◽  
Food Borne ◽  
Food Isolate

Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges, Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept for a short-read strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic tree. These metagenomics-derived outbreak strains were separated from sporadic cases as well as from another outbreak circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne outbreak investigation uniquely linking the food source using a metagenomics approach and this in a fast time frame.

scholarly journals Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

2017 ◽  
Vol 83 (16) ◽  
Author(s):  
Aaron M. Walsh ◽  
Fiona Crispie ◽  
Kareem Daari ◽  
Orla O'Sullivan ◽  
Jennifer C. Martin ◽  
...  
Keyword(s):  
Food Safety ◽  
Food Products ◽  
Strain Level ◽  
Milk Product ◽  
Shotgun Metagenomics ◽  
Short Read ◽  
Content Type ◽  
Read Alignment ◽  
Short Read Alignment ◽  
Metagenome Assembly

ABSTRACT The rapid detection of pathogenic strains in food products is essential for the prevention of disease outbreaks. It has already been demonstrated that whole-metagenome shotgun sequencing can be used to detect pathogens in food but, until recently, strain-level detection of pathogens has relied on whole-metagenome assembly, which is a computationally demanding process. Here we demonstrated that three short-read-alignment-based methods, i.e., MetaMLST, PanPhlAn, and StrainPhlAn, could accurately and rapidly identify pathogenic strains in spinach metagenomes that had been intentionally spiked with Shiga toxin-producing Escherichia coli in a previous study. Subsequently, we employed the methods, in combination with other metagenomics approaches, to assess the safety of nunu, a traditional Ghanaian fermented milk product that is produced by the spontaneous fermentation of raw cow milk. We showed that nunu samples were frequently contaminated with bacteria associated with the bovine gut and, worryingly, we detected putatively pathogenic E. coli and Klebsiella pneumoniae strains in a subset of nunu samples. Ultimately, our work establishes that short-read-alignment-based bioinformatics approaches are suitable food safety tools, and we describe a real-life example of their utilization. IMPORTANCE Foodborne pathogens are responsible for millions of illnesses each year. Here we demonstrate that short-read-alignment-based bioinformatics tools can accurately and rapidly detect pathogenic strains in food products by using shotgun metagenomics data. The methods used here are considerably faster than both traditional culturing methods and alternative bioinformatics approaches that rely on metagenome assembly; therefore, they can potentially be used for more high-throughput food safety testing. Overall, our results suggest that whole-metagenome sequencing can be used as a practical food safety tool to prevent diseases or to link outbreaks to specific food products.

The global refugee crisis and the career ecosystem

2019 ◽  
Vol 25 (1) ◽  
pp. 1-13
Author(s):  
Julia Richardson ◽  
Charlotte M. Karam ◽  
Fida Afiouni
Keyword(s):  
Media Coverage ◽  
Community Dynamics ◽  
Media Analysis ◽  
Host Community ◽  
Refugee Crisis ◽  
Content Type ◽  
Relevant Stakeholder ◽  
Media Reports ◽  
The Impact ◽  
Business Media

Purpose The purpose of this paper is to introduce this special issue about the “Impact of the Global Refugee Crisis on the Career Ecosystem” and summarise the key contributions of the included practitioner and scholarly papers which examine refugee business and labour market experiences. The paper also examines the impact of media reports to provide a broader understanding of the context within which the current refugee crisis is evolving. Design/methodology/approach The authors begin with a delineation of the concept of a career ecosystem in the context of refugee crises. The authors then employ this framing as a backdrop to engage in a basic analysis of business media coverage of the most recent Syrian refugee crisis, and a summary of the practitioner and scholarly papers. Findings The findings of the media analysis suggest major coverage differences between different groups of countries in the number of documents identified, the proposed aim of business engagement with refugees, and substance of the extracted statements generally. Research limitations/implications The analysis of business media coverage is rudimentary and intended only as a prompt for further conversations about how contemporary media commentary impacts on career opportunities for refugees and relevant stakeholder practices. Practical implications This paper demonstrates the importance of including broader considerations of refugee careers that explore the interaction and intersection with transnational and local ecosystem of labour markets while paying attention to the sociocultural and political refugee-host community dynamics. Originality/value This paper presents a more systems-oriented perspective and provides both practice and scholarly perspectives on the composite and dynamic nature of the refugee crisis on career ecosystems more broadly.

scholarly journals Reclassification of Bacteriovorax marinus as Halobacteriovorax marinus gen. nov., comb. nov. and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov.; description of Halobacteriovoraceae fam. nov. in the class Deltaproteobacteria

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 593-597 ◽  
Author(s):  
Susan F. Koval ◽  
Henry N. Williams ◽  
O. Colin Stine
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Strain Atcc ◽  
Content Type ◽  
Link Type ◽  
As Species ◽  
Previous Proposal

The taxonomic status of saltwater Bdellovibrio -like prokaryotic predators has been revised to assign species to Halobacteriovorax gen. nov. A reclassification of Bacteriovorax marinus as Halobacteriovorax marinus comb. nov. (type strain ATCC BAA-682T = DSM 15412T) and Bacteriovorax litoralis as Halobacteriovorax litoralis comb. nov. (type strain ATCC BAA-684T = DSM 15409T) is proposed. This revision is necessary because a previous proposal to retain saltwater isolates as species of Bacteriovorax and reclassify Bacteriovorax stolpii as Bacteriolyticum stolpii was not approved. The type species of a genus cannot be reassigned to another genus. Bacteriovorax stolpii is thus retained as the type species of Bacteriovorax and Halobacteriovorax marinus is the type species of Halobacteriovorax and of Halobacteriovoraceae fam. nov.

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections

2021 ◽  
Vol 70 (12) ◽  
Author(s):  
Letícia T. Oliveira ◽  
Lívia A. Alves ◽  
Erika N. Harth-Chu ◽  
Ryota Nomura ◽  
Kazuhiko Nakano ◽  
...  
Keyword(s):  
Streptococcus Mutans ◽  
Type Species ◽  
Virulence Gene ◽  
Common Species ◽  
Oral Microbiome ◽  
Nucleotide Polymorphisms ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Coding Regions ◽  
Link Type

Introduction. Streptococcus mutans , a common species of the oral microbiome, expresses virulence genes promoting cariogenic dental biofilms, persistence in the bloodstream and cardiovascular infections. Gap statement. Virulence gene expression is variable among S. mutans strains and controlled by the transcription regulatory systems VicRK and CovR. Aim. This study investigates polymorphisms in the vicRK and covR loci in S. mutans strains isolated from the oral cavity or from the bloodstream, which were shown to differ in expression of covR, vicRK and downstream genes. Methodology. The transcriptional activities of covR, vicR and vicK were compared by RT-qPCR between blood and oral strains after exposure to human serum. PCR-amplified promoter and/or coding regions of covR and vicRK of 18 strains (11 oral and 7 blood) were sequenced and compared to the reference strain UA159. Results. Serum exposure significantly reduced covR and vicR/K transcript levels in most strains (P<0.05), but reductions were higher in oral than in blood strains. Single-nucleotide polymorphisms (SNPs) were detected in covR regulatory and coding regions, but SNPs affecting the CovR effector domain were only present in two blood strains. Although vicR was highly conserved, vicK showed several SNPs, and SNPs affecting VicK regions important for autokinase activity were found in three blood strains. Conclusions. This study reveals transcriptional and structural diversity in covR and vicR/K, and identifies polymorphisms of functional relevance in blood strains, indicating that covR and vicRK might be important loci for S. mutans adaptation to host selective pressures associated with virulence diversity.

Accountable care organizations: a strategy for future success?

2018 ◽  
Vol 21 (2) ◽  
pp. 113-121
Author(s):  
Jeffrey Harrison ◽  
Aaron Spaulding ◽  
Debra A. Harrison
Keyword(s):  
Community Dynamics ◽  
Accountable Care Organizations ◽  
Accountable Care ◽  
Healthcare Organizations ◽  
American Hospital ◽  
American Hospital Association ◽  
Content Type ◽  
For Profit ◽  
Annual Survey ◽  
Final Rule

Purpose The purpose of this paper is to assess the community dynamics and organizational characteristics of US hospitals that participate in accountable care organizations (ACO). Design/methodology/approach Data were obtained from the 2015 American Hospital Association annual survey and the 2015 medicare final rule standardizing file. The study evaluated 785 hospitals which operate ACO in contrast to 1,446 hospitals without an ACO. Findings In total, 89 percent of hospitals using ACO’s are located in urban communities and 87 percent are not-for-profit. Hospitals with a higher case mix index are more likely to have an ACO. Practical implications ACOs allow healthcare organizations to expand their geographic markets, achieve greater efficiencies, and enhance the development of new clinical services. They also shift the focus of care from acute care hospitalization to the full continuum of care. Originality/value This research found ACOs with hospital and physician networks are an effective mechanism to control healthcare costs and reduce medical errors.

scholarly journals Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun Metagenomics

2018 ◽  
Vol 6 (14) ◽  
Author(s):  
Natacha Couto ◽  
Monika A. Chlebowicz ◽  
Erwin C. Raangs ◽  
Alex W. Friedrich ◽  
John W. Rossen
Keyword(s):  
Nosocomial Infections ◽  
Complete Genome ◽  
Clinical Sample ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
European Countries ◽  
Genome Sequences ◽  
Shotgun Metagenomics ◽  
Content Type ◽  
Staphylococcus Haemolyticus

ABSTRACT The emergence of nosocomial infections by multidrug-resistant Staphylococcus haemolyticus isolates has been reported in several European countries. Here, we report the first two complete genome sequences of S. haemolyticus sequence type 25 (ST25) isolates 83131A and 83131B. Both isolates were isolated from the same clinical sample and were first identified through shotgun metagenomics.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

Sign in / Sign up

Export Citation Format

Share Document