About
55
Publications
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Introduction
Clinical ecologist | Gut microbiome - immune interactions in cancer immunotherapy and solid organ transplantation
Current institution
Additional affiliations
June 2020 - present
September 2011 - June 2016
Universitat Politècnica de Catalunya | Institute of Marine Sciences | CBTM CNRS |
Position
- PhD Student
Description
- Title: The Structure and Dynamics of Complex Microbe-Host Interaction Networks. Supervisor: Jose M Montoya.
Education
September 2009 - September 2010
September 2009 - September 2011
September 2005 - September 2009
Publications
Publications (55)
Background/Objectives: Tacrolimus dosing traditionally relies on therapeutic drug monitoring in whole blood, while assessment in plasma may better reflect its effect and reveal overdosing impacting health-related quality of life (HRQoL). Methods: In this cross-sectional study, 898 kidney transplant recipients (KTRs) who were at least 12 months post...
Host‐associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from systems biased towards animal models and humans.
While many studies on non‐model and wild animals have characterised the taxonomic diversity of their microbiomes, few have investigated the functional potential of these...
Objective
Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, the relationship with overall survival in specific diseases has not been extensively studied. In the curren...
Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients, but the gut microbiome of lung transplant recipients has not been extensively explored. We assessed the gut microbiome in 64 fecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transplant recipients aft...
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal...
Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome changes during ICB is urgently needed. Here through longitudinal microbiome profiling of 175 patients treated with ICB for advanced...
Host-associated microbiomes are thought to play a key role in host physiology and fitness, but this conclusion mainly derives from studies of a handful of animal models and humans. To test the generality of this conclusion, studies in non-model and wild animals are needed. However, whilst microbiome taxonomic diversity has recently received much at...
Background
The pathogenetic mechanisms that lead to IBD flares are unknown and the absence of reliable predictive biomarkers results in a therapeutic approach focused on treating active flares rather than prevention. While IBD is known to be associated to changes in gut microbiota, the longitudinal dynamics of the microbiome in relation to disease...
Aims
Despite treatment advancements, cardiovascular disease remains a leading cause of death worldwide. Identifying new targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with coronary artery disease (CAD), however our understanding of specific changes during CAD development remains limite...
Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from feca...
Background
Gut dysbiosis has been associated with impaired outcomes in liver and kidney transplant recipients but the gut microbiome of lung transplant recipients has not been previously studied.
Methods
We assessed the gut microbiome in 64 faecal samples from end-stage lung disease patients before transplantation and 219 samples from lung transpl...
Background: KRAS-mutated non-small cell lung cancer (NSCLC) is associated with a poor prognosis to standard therapies. Despite advances of immune checkpoint inhibitors (ICIs), not all patients show durable responses. In this study, we aim to identify associations between ICI-response and the gut microbiome in patients with KRAS-mutated NSCLC.
Metho...
Objective
Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general population, the relation with overall survival in specific diseases has not been extensively studied. In the current st...
Rationale
Despite significant progress in treatment strategies, cardiovascular disease remains a leading cause of death worldwide. Identifying new potential targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with the development of coronary artery disease (CAD), however our understanding o...
Multiple clinical trials targeting the gut microbiome are being conducted to optimize treatment outcomes for immune checkpoint blockade (ICB). To improve the success of these interventions, understanding gut microbiome dynamics during ICB is urgently needed. Through longitudinal shotgun metagenomics profiling in 175 patients treated with ICB for ad...
Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or...
Background
Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of melanoma and other cancers. However, no reliable biomarker of survival or response has entered the clinic to identify those patients with melanoma who are most likely to benefit from ICIs. Glycosylation affects proteins and lipids’ structure and functions. Tumours a...
Importance:
Immune checkpoint blockade (ICB) has improved the survival of patients with advanced melanoma. Durable responses are observed for 40% to 60% of patients, depending on treatment regimens. However, there is still large variability in the response to treatment with ICB, and patients experience a range of immune-related adverse events of d...
Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. We investigated the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal sam...
Background
Host intestinal immune gene signatures and microbial dysregulations expose potential mechanisms in the pathogenesis of inflammatory bowel diseases (IBD). Profiling of mucosa-attached microbiota allows the understanding of locally present microbial communities and their immediate impact on the host. This study aimed to comprehensively exa...
Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and fatigue, are common. We hypothesise that the gut microbiome might play a role in the pathophysiology of the (non-)motor symptoms in dystonia via the gut–brain axis. This exploratory...
Background
Inflammation can modulate tumour growth and progression, and influence clinical response to treatment. We investigated the potential of circulating inflammatory proteins for response stratification of immune checkpoint inhibitor (ICI) therapy for advanced melanoma.
Methods
Study subjects were 87 patients with unresectable stage III or I...
Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival rates after transplantation vary considerably. There is now increasing evidence that the gut microbiome is linked to the survival of patients undergoing hematopoietic cell transplant, yet little is known about the role of the gut microbiome in solid o...
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in host genetics, diets, environments and medications but it could also emerge from fundamental ecological forces that shape microbiota more...
Dysregulation of gut mucosal host-microbe interactions is a central feature of inflammatory bowel disease (IBD). To study tissue-specific interactions, we performed transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 696 intestinal biopsies derived from 353 patients with IBD and controls. Analysis of transcript-bacteria interactions...
The gut microbiome is associated with diverse diseases1–3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virule...
The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on the specific microbiome characteristics linked to the clinical benefits of ICIs. We performed shotgun metagenomic sequencing of stool samples collected before ICI initiation from five ob...
Human gut microbial dynamics are highly individualized, making it challenging to link microbiota to health and to design universal microbiome therapies. This individuality is typically attributed to variation in diets, environments, and medications, but it could also emerge from fundamental ecological forces that shape primate microbiota more gener...
Baboons inform on human gut microbiota
Commensal bacteria are found throughout an organism, but it is not known whether associations between gut bacteria and their host are heritable. Grieneisen et al. examined changes in the microbiomes of 585 wild baboons from fecal samples collected over 14 years (see the Perspective by Cortes-Ortiz and Amato)....
Background
The pathogenesis of inflammatory bowel diseases is characterized by gastrointestinal dysbiosis. Small molecules -or metabolites- present in feces can improve our understanding of host and microbes’ interactions. By exploring the relationship between host genetics, gut microbiota, and fecal metabolites composition from 500 patients with I...
Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival post-transplantation varies considerably. There is now increasing evidence that the gut microbiome is linked to the survival of hematopoietic cell transplant patients, yet little is known about the role of the gut microbiome in solid organ transplanta...
The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence f...
The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence f...
Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Her...
To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross-sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical fun...
Classic evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes, and high partner fidelity between host species and their vertically transmitted microbe...
In addition to the processes structuring free‐living communities, host‐associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host‐specific factors, often spanning multiple levels of biological organization. Cu...
Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of spon...
Additionally to the processes structuring free-living communities, animal-associated microbial communities, so-called microbiotas, are directly or indirectly shaped by the animal host. This results in a hierarchical data structure where samples are nested under one or several variables representing host-specific features. Previous statistical tools...
The long-term stability of microbiomes is crucial as the persistent occurrence of beneficial microbes and their associated functions ensure host health. Microbiomes are highly diverse and dynamic, but are they complex to the point of being impossible to understand? We present an approach that while embracing this complexity it allows to identifying...
Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contribut...
Representative sequences and taxonomy of OTUs.
Supplementary Figures 1-8 and Supplementary Tables 1-2
Metadata for sponge samples analysed in the current study.
Diversity and richness of sponge species.
Microbes are known to form intricate and intimate relationships with most animal and plant taxa. Microbe--host symbiotic associations are poorly explored in comparison with other species interaction networks. The current paradigm on symbiosis research stems from species-poor systems where pairwise and reciprocally specialized interactions between a...
Among nest-holding fish, males often choose nest sites according to their own body size (i.e. size-assortative nest choice). In most cases, this can be explained by intrasexual competition. However, a few studies, for example on a marine population of the sand goby, Pomatoschistus minutus, have found a size-assortative nest preference, even when in...
