Catherine Ngom-bru - Academia.edu (original) (raw)

Papers by Catherine Ngom-bru

Research paper thumbnail of A temporal view of the water kefir microbiota and flavour attributes

Innovative Food Science & Emerging Technologies

Research paper thumbnail of A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning

Research paper thumbnail of C: Gut microbiota: methodological aspects to describe taxonomy and functionality

The human gut is populated by a rich and diverse microbiota that has been described as a human me... more The human gut is populated by a rich and diverse microbiota that has been described as a human metabolic organ. Its composition has an impact on the health status of the host and could be the target or effector of dietary health effects. The advent of high-throughput sequencing technologies and their integration with advanced analysis methods enables the development of new approaches to characterize the gut microbiota composition and initiates the understanding of its functionality.These technological aspects are not necessarily the limiting factor to success-fully identify biological correlations between gut microbiota, diet and health status, as there are other very import-ant aspects. The aim of this article is to address the gut microbiota characterization methodologies, highlight some advantages and challenges, and give our opinion on how critical the sampling and the study design are.

Research paper thumbnail of Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation

Genes, 2021

Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking i... more Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS. Ongoing work towards standardization of wet lab including sequencing protocols, following guidelines from the regulatory authorities and international standardization efforts make the technology more and more accessible. However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions. There are multiple bioinformatics software and pipelines developed to handle such information. Nevertheless, little consensus exists on a...

Research paper thumbnail of Implications of mobile genetic elements for Salmonella enterica single nucleotide polymorphism subtyping and source tracking investigations

Applied and Environmental Microbiology, 2019

Single nucleotide polymorphisms (SNPs) are widely used for whole genome sequencing (WGS)-based su... more Single nucleotide polymorphisms (SNPs) are widely used for whole genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using Salmonella enterica as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion elements (IS), integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of S. enterica. We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018. The median total length of chromosomal MGEs accounted for 2.5% of a typical S. enterica chromosome. Sixty-eight point nine percent of the 990 analyzed S. enterica isolates contained at least one assembled...

Research paper thumbnail of A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

Frontiers in Microbiology, 2018

Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete ... more Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.

Research paper thumbnail of Effect of Formula Containing Lactobacillus Reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section

Journal of pediatric gastroenterology and nutrition, Jan 28, 2016

Microbiota modulation by probiotics in infants born by cesarean (C)-section is poorly understood.... more Microbiota modulation by probiotics in infants born by cesarean (C)-section is poorly understood. We aimed at assessing the response of C-section-delivered infant microbiota to a formula containing L. reuteri DSM 17938 and comparing it with that of vaginally-delivered infants. Infants delivered by C-section (C) and vaginally (V) were randomized to receive either control formula (CCt, n = 10; VCt, n = 10) or the same formula containing L. reuteri (CLr, n = 11; VLr, n = 9) within 72 hours following birth. Stool samples were collected at 2 weeks and 4 months of age. Microbial DNA was extracted, amplified and pyrosequenced. The phylogenetic profiles of the CLr, VCt and VLr microbiota were not significantly different at any age, but diverged from that of CCt at 2 weeks. Compared with VCt, CCt displayed lower Bifidobacterium and higher Enterobacter, unclassified Enterobacteriaceae, Enterococcus, Clostridium and unclassified Clostridiaceae relative abundance at 2 weeks, as well as lower Co...

Research paper thumbnail of Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh

EBioMedicine, 2016

Background: Antibiotic resistance is rising in important bacterial pathogens. Phage therapy (PT),... more Background: Antibiotic resistance is rising in important bacterial pathogens. Phage therapy (PT), the use of bacterial viruses infecting the pathogen in a species-specific way, is a potential alternative. Method: T4-like coliphages or a commercial Russian coliphage product or placebo was orally given over 4 days to Bangladeshi children hospitalized with acute bacterial diarrhea. Safety of oral phage was assessed clinically and by functional tests; coliphage and Escherichia coli titers and enteropathogens were determined in stool and quantitative diarrhea parameters (stool output, stool frequency) were measured. Stool microbiota was studied by 16S rRNA gene sequencing; the genomes of four fecal Streptococcus isolates were sequenced. Findings: No adverse events attributable to oral phage application were observed (primary safety outcome). Fecal coliphage was increased in treated over control children, but the titers did not show substantial intestinal phage replication (secondary microbiology outcome). 60% of the children suffered from a microbiologically proven E. coli diarrhea; the most frequent diagnosis was ETEC infections. Bacterial co-pathogens were also detected. Half of the patients contained phage-susceptible E. coli colonies in the stool. E. coli represented less than 5% of fecal bacteria. Stool ETEC titers showed only a short-lived peak and were otherwise close to the replication threshold determined for T4 phage in vitro. An interim analysis after the enrollment of 120 patients showed no amelioration in quantitative diarrhea parameter by PT over standard care (tertiary clinical outcome). Stool microbiota was characterized by an overgrowth with Streptococcus belonging to the Streptococcus gallolyticus and Streptococcus salivarius species groups, their abundance correlated with quantitative diarrhea outcome, but genome sequencing did not identify virulence genes. Interpretation: Oral coliphages showed a safe gut transit in children, but failed to achieve intestinal amplification and to improve diarrhea outcome, possibly due to insufficient phage coverage and too low E. coli pathogen titers requiring higher oral phage doses. More knowledge is needed on in vivo phage-bacterium interaction and the role of E. coli in childhood diarrhea for successful PT.

Research paper thumbnail of Live and heat-treated probiotics differently modulate IL10 mRNA stabilization and microRNA expression

Journal of Allergy and Clinical Immunology, 2016

have PA despite peanut consumption versus 158 cases of PA (449 3 0.353) if peanuts were avoided. ... more have PA despite peanut consumption versus 158 cases of PA (449 3 0.353) if peanuts were avoided. One hundred ten cases (158 2 48) of PA would be prevented by peanut consumption in the group with positive SPT responses. This is a 24.7% absolute reduction. The projected incidence of PA in LEAP-eligible children with SCORAD scores of greater than 40 or egg allergy who, before the LEAP study, would have routinely avoided peanut would be 488 cases (330 in the group with negative SPT responses and 158 in the group with positive SPT responses). The total number of cases of PA that could be avoided in Ireland using the LEAP protocol per annum would be 348 (238 LEAP-eligible Irish children with negative SPT negative responses and 110 LEAP-eligible Irish children with positive SPT responses) (see Table E2 in this article's Online Repository at www.jacionline.org). This represents a relative reduction of 71% in the defined high-risk groups of infants. There would be a substantial effect on the incidence of PA in the 2,932 Irish children who meet the 2 most objective LEAP criteria of severe AD with SCORAD scores of greater than 40 or existing egg allergy at 6 months, with a relative reduction in the incidence of PA of 71%. The population-level effect is less dramatic (29% relative reduction) because LEAP-defined high-risk children are only a minority of cases (488/1202 cases per annum). Our report has limitations relating mainly to the use of a slightly different case definition for egg allergy to those used in the LEAP study. However, all Irish cases were in infants with challenge-proved egg allergy rather than merely egg-sensitized infants. The only national data for PA relate to challengeproved PA at 2 years compared with the LEAP definition of PA at 5 years (60 months). Although PA can resolve, this is in only a minority of cases (20%), and therefore we have not made any specific estimates of the likely rate of PA in Ireland at 6 years of age to make a direct comparison with LEAP data. Our calculations presume full implementation of the LEAP protocols. However, these limitations are offset by the robustness of the existing LEAP data and published BASELINE data, by the similarity of the estimates of Irish and British rates of PA and by the broad socioeconomic similarities of the 2 countries. The LEAP study has shown that peanut consumption is safe and well tolerated. However, community implementation would demand huge additional resources at all levels of health care. Further studies need to be performed to assess many unresolved aspects of peanut introduction. The LEAP study has already prompted international organizations to reexamine their allergy prevention advice. 7 Exercises such as we report here could be done with the data of any country that has reliable national prevalence data for allergic conditions in infancy to better inform pragmatic national policy changes and appropriate resource allocation in countries with different prevalences of PA. We thank the parents and children and our colleagues in the BASELINE study and our allergy colleagues K.

Research paper thumbnail of Rate of establishing the gut microbiota in infancy has consequences for future health

Gut Microbes, 2015

al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration an... more al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. MBio

Research paper thumbnail of T4 phages against Escherichia coli diarrhea: Potential and problems

Virology, 2009

A combination of in vitro and in vivo experiments with comparative phage genomics was used for th... more A combination of in vitro and in vivo experiments with comparative phage genomics was used for the rational design of a phage cocktail against E. coli diarrhea. Orally applied T4 coliphages representing three different subgroups (T4-, RB49-and JS98-like phages) had no negative impact on the murine gut microbiota. T4 phages were found with high titers in the cecum and colon and lower titers in the small intestine, but were not detected in the blood, liver or spleen. No adverse effects were observed after one-month exposure to phage nor were serum anti-T4 antibodies detected. T4 phages belonging to the same subgroup showed closely related genomes that differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49 reference) insertion/deletions mostly representing single small ORFs. Bioinformatic analysis did not reveal undesired genes in the T4 genomes. Sequence variability was seen over the tail fibre genes, but the variability did not correlate with phage host range. The investigated T4 phages were not only species-but also strainspecific, necessitating the use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover half to two thirds of E. coli strains representing the five main pathotypes isolated from diarrhea patients.

Research paper thumbnail of Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

Nature Medicine, 2014

Metabolites from intestinal microbiota are key determinants of host-microbe mutualism and, conseq... more Metabolites from intestinal microbiota are key determinants of host-microbe mutualism and, consequently, the health or disease of the intestinal tract. However, whether such host-microbe crosstalk influences inflammation in peripheral tissues, such as the lung, is poorly understood. We found that dietary fermentable fiber content changed the composition of the gut and lung microbiota, in particular by altering the ratio of Firmicutes to Bacteroidetes. The gut microbiota metabolized the fiber, consequently increasing the concentration of circulating short-chain fatty acids (SCFAs). Mice fed a high-fiber diet had increased circulating levels of SCFAs and were protected against allergic inflammation in the lung, whereas a low-fiber diet decreased levels of SCFAs and increased allergic airway disease. Treatment of mice with the SCFA propionate led to alterations in bone marrow hematopoiesis that were characterized by enhanced generation of macrophage and dendritic cell (DC) precursors and subsequent seeding of the lungs by DCs with high phagocytic capacity but an impaired ability to promote T helper type 2 (T H 2) cell effector function. The effects of propionate on allergic inflammation were dependent on G protein-coupled receptor 41 (GPR41, also called free fatty acid receptor 3 or FFAR3), but not GPR43 (also called free fatty acid receptor 2 or FFAR2). Our results show that dietary fermentable fiber and SCFAs can shape the immunological environment in the lung and influence the severity of allergic inflammation.

Research paper thumbnail of Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli

Journal of Bacteriology, 2007

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewa... more Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene ( g23 ) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes wer...

Research paper thumbnail of Infant gut microbiota is protective against cow's milk allergy in mice despite immature ileal T-cell response

FEMS Microbiology Ecology, 2011

Faecal microbiota of healthy infant displays a large abundance of Bifidobacterium spp. and Bacter... more Faecal microbiota of healthy infant displays a large abundance of Bifidobacterium spp. and Bacteroides spp. Although some studies have reported an association between these two genera and allergy, these findings remain a subject of debate. Using a gnotobiotic mouse model of cow's milk allergy, we investigated the impact of an infant gut microbiotamainly composed of Bifidobacterium and Bacteroides spp.on immune activation and allergic manifestations. The transplanted microbiota failed to restore an ileal T-cell response similar to the one observed in conventional mice. This may be due to the low bacterial translocation into Peyer's patches in gnotobiotic mice. The allergic response was then monitored in germ-free, gnotobiotic, and conventional mice after repeated oral sensitization with whey proteins and cholera toxin. Colonized mice displayed a lower drop of rectal temperature upon oral challenge with b-lactoglobulin, lower plasma mMCP-1, and lower anti-BLG IgG1 than germ-free mice. The foxp3 gene was highly expressed in the ileum of both colonized mice that were protected against allergy. This study is the first demonstration that a transplanted healthy infant microbiota mainly composed of Bifidobacterium and Bacteroides had a protective impact on sensitization and food allergy in mice despite altered T-cell response in the ileum.

Research paper thumbnail of Phylogenetic, Functional and Safety Features of 1950s B. infantis Strains

Microorganisms, 2022

Strains of Bifidobacterium longum subsp. infantis (B. infantis) are amongst the first to colonize... more Strains of Bifidobacterium longum subsp. infantis (B. infantis) are amongst the first to colonize the infant gut, partly due to their capacity to metabolize complex human milk oligosaccharides (HMO), and are proposed to play a key role in the development of the infant gut. Since early life, B. infantis supplementation is of high interest, and detailed phylogenetic, functional and safety characterization of the selected strains should be pursued. Using a combination of long and short-read sequencing technologies, we first decipher the genetic distance between different isolates of the same B. infantis strain. Using the same approach, we show that several publicly available genomes recapitulate this strain-level distance as compared to two of the first strains obtained in the 1950s. Furthermore, we demonstrate that the two 1950s B. infantis strains display different functional and safety attributes, as ATCC 15697 is resistant to streptomycin and shows a preference towards lacto-N-tetr...

Research paper thumbnail of Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity

mBio, 2015

We found that the relatively simple microbiota of young infants shifts predictably to a more matu... more We found that the relatively simple microbiota of young infants shifts predictably to a more mature anaerobic microbiota during infancy and the dynamics of this shift are influenced by environmental factors. In this longitudinal study of 75 infants, we demonstrate high interindividual variability within the normal range of birth outcomes, especially in the rate of microbiota progression. Most had acquired a microbiota profile high in Bifidobacterium and Collinsella by 6 months of age, but the time point of this acquisition was later in infants delivered by caesarean section and those born after a shorter duration of gestation. Independently of the delivery mode and gestation duration, infants who acquired a profile high in Bifidobacterium and Collinsella at a later age had lower adiposity at 18 months of age. IMPORTANCE This study shows that the acquisition of the early microbiota is strongly influenced by environmental factors such as the delivery mode and duration of gestation, even in healthy neonates. The composition of the early microbiota has been linked with long-lasting effects on health and disease. Here we show that the rate of acquisition of certain microbiota predicts adiposity at 18 months of age and so potentially the risk of later obesity. . 2015. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. mBio 6(1):e02419-14.

Research paper thumbnail of T4 phages against Escherichia coli diarrhea: Potential and problems

Virology, 2009

A combination of in vitro and in vivo experiments with comparative phage genomics was used for th... more A combination of in vitro and in vivo experiments with comparative phage genomics was used for the rational design of a phage cocktail against E. coli diarrhea. Orally applied T4 coliphages representing three different subgroups (T4-, RB49-and JS98-like phages) had no negative impact on the murine gut microbiota. T4 phages were found with high titers in the cecum and colon and lower titers in the small intestine, but were not detected in the blood, liver or spleen. No adverse effects were observed after one-month exposure to phage nor were serum anti-T4 antibodies detected. T4 phages belonging to the same subgroup showed closely related genomes that differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49 reference) insertion/deletions mostly representing single small ORFs. Bioinformatic analysis did not reveal undesired genes in the T4 genomes. Sequence variability was seen over the tail fibre genes, but the variability did not correlate with phage host range. The investigated T4 phages were not only species-but also strainspecific, necessitating the use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover half to two thirds of E. coli strains representing the five main pathotypes isolated from diarrhea patients.

Research paper thumbnail of Effect of Lactobacillus rhamnosus CGMCC1.3724 supplementation on weight loss and maintenance in obese men and women

British Journal of Nutrition, 2014

The present study investigated the impact of a Lactobacillus rhamnosus CGMCC1.3724 (LPR) suppleme... more The present study investigated the impact of a Lactobacillus rhamnosus CGMCC1.3724 (LPR) supplementation on weight loss and maintenance in obese men and women over 24 weeks. In a double-blind, placebo-controlled, randomised trial, each subject consumed two capsules per d of either a placebo or a LPR formulation (1.6 × 10(8) colony-forming units of LPR/capsule with oligofructose and inulin). Each group was submitted to moderate energy restriction for the first 12 weeks followed by 12 weeks of weight maintenance. Body weight and composition were measured at baseline, at week 12 and at week 24. The intention-to-treat analysis showed that after the first 12 weeks and after 24 weeks, mean weight loss was not significantly different between the LPR and placebo groups when all the subjects were considered. However, a significant treatment × sex interaction was observed. The mean weight loss in women in the LPR group was significantly higher than that in women in the placebo group (P = 0.02) after the first 12 weeks, whereas it was similar in men in the two groups (P= 0.53). Women in the LPR group continued to lose body weight and fat mass during the weight-maintenance period, whereas opposite changes were observed in the placebo group. Changes in body weight and fat mass during the weight-maintenance period were similar in men in both the groups. LPR-induced weight loss in women was associated not only with significant reductions in fat mass and circulating leptin concentrations but also with the relative abundance of bacteria of the Lachnospiraceae family in faeces. The present study shows that the Lactobacillus rhamnosus CGMCC1.3724 formulation helps obese women to achieve sustainable weight loss.

Research paper thumbnail of Narcisse: a mirror view of conserved syntenies

Nucleic Acids Research, 2007

New methods and tools are needed to exploit the unprecedented source of information made availabl... more New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.

Research paper thumbnail of Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli

Journal of Bacteriology, 2007

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewa... more Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.

Research paper thumbnail of A temporal view of the water kefir microbiota and flavour attributes

Innovative Food Science & Emerging Technologies

Research paper thumbnail of A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning

Research paper thumbnail of C: Gut microbiota: methodological aspects to describe taxonomy and functionality

The human gut is populated by a rich and diverse microbiota that has been described as a human me... more The human gut is populated by a rich and diverse microbiota that has been described as a human metabolic organ. Its composition has an impact on the health status of the host and could be the target or effector of dietary health effects. The advent of high-throughput sequencing technologies and their integration with advanced analysis methods enables the development of new approaches to characterize the gut microbiota composition and initiates the understanding of its functionality.These technological aspects are not necessarily the limiting factor to success-fully identify biological correlations between gut microbiota, diet and health status, as there are other very import-ant aspects. The aim of this article is to address the gut microbiota characterization methodologies, highlight some advantages and challenges, and give our opinion on how critical the sampling and the study design are.

Research paper thumbnail of Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation

Genes, 2021

Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking i... more Whole genome sequencing (WGS) has arisen as a powerful tool to perform pathogen source tracking in the food industry thanks to several developments in recent years. However, the cost associated to this technology and the degree of expertise required to accurately process and understand the data has limited its adoption at a wider scale. Additionally, the time needed to obtain actionable information is often seen as an impairment for the application and use of the information generated via WGS. Ongoing work towards standardization of wet lab including sequencing protocols, following guidelines from the regulatory authorities and international standardization efforts make the technology more and more accessible. However, data analysis and results interpretation guidelines are still subject to initiatives coming from distinct groups and institutions. There are multiple bioinformatics software and pipelines developed to handle such information. Nevertheless, little consensus exists on a...

Research paper thumbnail of Implications of mobile genetic elements for Salmonella enterica single nucleotide polymorphism subtyping and source tracking investigations

Applied and Environmental Microbiology, 2019

Single nucleotide polymorphisms (SNPs) are widely used for whole genome sequencing (WGS)-based su... more Single nucleotide polymorphisms (SNPs) are widely used for whole genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using Salmonella enterica as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion elements (IS), integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of S. enterica. We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018. The median total length of chromosomal MGEs accounted for 2.5% of a typical S. enterica chromosome. Sixty-eight point nine percent of the 990 analyzed S. enterica isolates contained at least one assembled...

Research paper thumbnail of A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

Frontiers in Microbiology, 2018

Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete ... more Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.

Research paper thumbnail of Effect of Formula Containing Lactobacillus Reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section

Journal of pediatric gastroenterology and nutrition, Jan 28, 2016

Microbiota modulation by probiotics in infants born by cesarean (C)-section is poorly understood.... more Microbiota modulation by probiotics in infants born by cesarean (C)-section is poorly understood. We aimed at assessing the response of C-section-delivered infant microbiota to a formula containing L. reuteri DSM 17938 and comparing it with that of vaginally-delivered infants. Infants delivered by C-section (C) and vaginally (V) were randomized to receive either control formula (CCt, n = 10; VCt, n = 10) or the same formula containing L. reuteri (CLr, n = 11; VLr, n = 9) within 72 hours following birth. Stool samples were collected at 2 weeks and 4 months of age. Microbial DNA was extracted, amplified and pyrosequenced. The phylogenetic profiles of the CLr, VCt and VLr microbiota were not significantly different at any age, but diverged from that of CCt at 2 weeks. Compared with VCt, CCt displayed lower Bifidobacterium and higher Enterobacter, unclassified Enterobacteriaceae, Enterococcus, Clostridium and unclassified Clostridiaceae relative abundance at 2 weeks, as well as lower Co...

Research paper thumbnail of Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh

EBioMedicine, 2016

Background: Antibiotic resistance is rising in important bacterial pathogens. Phage therapy (PT),... more Background: Antibiotic resistance is rising in important bacterial pathogens. Phage therapy (PT), the use of bacterial viruses infecting the pathogen in a species-specific way, is a potential alternative. Method: T4-like coliphages or a commercial Russian coliphage product or placebo was orally given over 4 days to Bangladeshi children hospitalized with acute bacterial diarrhea. Safety of oral phage was assessed clinically and by functional tests; coliphage and Escherichia coli titers and enteropathogens were determined in stool and quantitative diarrhea parameters (stool output, stool frequency) were measured. Stool microbiota was studied by 16S rRNA gene sequencing; the genomes of four fecal Streptococcus isolates were sequenced. Findings: No adverse events attributable to oral phage application were observed (primary safety outcome). Fecal coliphage was increased in treated over control children, but the titers did not show substantial intestinal phage replication (secondary microbiology outcome). 60% of the children suffered from a microbiologically proven E. coli diarrhea; the most frequent diagnosis was ETEC infections. Bacterial co-pathogens were also detected. Half of the patients contained phage-susceptible E. coli colonies in the stool. E. coli represented less than 5% of fecal bacteria. Stool ETEC titers showed only a short-lived peak and were otherwise close to the replication threshold determined for T4 phage in vitro. An interim analysis after the enrollment of 120 patients showed no amelioration in quantitative diarrhea parameter by PT over standard care (tertiary clinical outcome). Stool microbiota was characterized by an overgrowth with Streptococcus belonging to the Streptococcus gallolyticus and Streptococcus salivarius species groups, their abundance correlated with quantitative diarrhea outcome, but genome sequencing did not identify virulence genes. Interpretation: Oral coliphages showed a safe gut transit in children, but failed to achieve intestinal amplification and to improve diarrhea outcome, possibly due to insufficient phage coverage and too low E. coli pathogen titers requiring higher oral phage doses. More knowledge is needed on in vivo phage-bacterium interaction and the role of E. coli in childhood diarrhea for successful PT.

Research paper thumbnail of Live and heat-treated probiotics differently modulate IL10 mRNA stabilization and microRNA expression

Journal of Allergy and Clinical Immunology, 2016

have PA despite peanut consumption versus 158 cases of PA (449 3 0.353) if peanuts were avoided. ... more have PA despite peanut consumption versus 158 cases of PA (449 3 0.353) if peanuts were avoided. One hundred ten cases (158 2 48) of PA would be prevented by peanut consumption in the group with positive SPT responses. This is a 24.7% absolute reduction. The projected incidence of PA in LEAP-eligible children with SCORAD scores of greater than 40 or egg allergy who, before the LEAP study, would have routinely avoided peanut would be 488 cases (330 in the group with negative SPT responses and 158 in the group with positive SPT responses). The total number of cases of PA that could be avoided in Ireland using the LEAP protocol per annum would be 348 (238 LEAP-eligible Irish children with negative SPT negative responses and 110 LEAP-eligible Irish children with positive SPT responses) (see Table E2 in this article's Online Repository at www.jacionline.org). This represents a relative reduction of 71% in the defined high-risk groups of infants. There would be a substantial effect on the incidence of PA in the 2,932 Irish children who meet the 2 most objective LEAP criteria of severe AD with SCORAD scores of greater than 40 or existing egg allergy at 6 months, with a relative reduction in the incidence of PA of 71%. The population-level effect is less dramatic (29% relative reduction) because LEAP-defined high-risk children are only a minority of cases (488/1202 cases per annum). Our report has limitations relating mainly to the use of a slightly different case definition for egg allergy to those used in the LEAP study. However, all Irish cases were in infants with challenge-proved egg allergy rather than merely egg-sensitized infants. The only national data for PA relate to challengeproved PA at 2 years compared with the LEAP definition of PA at 5 years (60 months). Although PA can resolve, this is in only a minority of cases (20%), and therefore we have not made any specific estimates of the likely rate of PA in Ireland at 6 years of age to make a direct comparison with LEAP data. Our calculations presume full implementation of the LEAP protocols. However, these limitations are offset by the robustness of the existing LEAP data and published BASELINE data, by the similarity of the estimates of Irish and British rates of PA and by the broad socioeconomic similarities of the 2 countries. The LEAP study has shown that peanut consumption is safe and well tolerated. However, community implementation would demand huge additional resources at all levels of health care. Further studies need to be performed to assess many unresolved aspects of peanut introduction. The LEAP study has already prompted international organizations to reexamine their allergy prevention advice. 7 Exercises such as we report here could be done with the data of any country that has reliable national prevalence data for allergic conditions in infancy to better inform pragmatic national policy changes and appropriate resource allocation in countries with different prevalences of PA. We thank the parents and children and our colleagues in the BASELINE study and our allergy colleagues K.

Research paper thumbnail of Rate of establishing the gut microbiota in infancy has consequences for future health

Gut Microbes, 2015

al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration an... more al. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. MBio

Research paper thumbnail of T4 phages against Escherichia coli diarrhea: Potential and problems

Virology, 2009

A combination of in vitro and in vivo experiments with comparative phage genomics was used for th... more A combination of in vitro and in vivo experiments with comparative phage genomics was used for the rational design of a phage cocktail against E. coli diarrhea. Orally applied T4 coliphages representing three different subgroups (T4-, RB49-and JS98-like phages) had no negative impact on the murine gut microbiota. T4 phages were found with high titers in the cecum and colon and lower titers in the small intestine, but were not detected in the blood, liver or spleen. No adverse effects were observed after one-month exposure to phage nor were serum anti-T4 antibodies detected. T4 phages belonging to the same subgroup showed closely related genomes that differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49 reference) insertion/deletions mostly representing single small ORFs. Bioinformatic analysis did not reveal undesired genes in the T4 genomes. Sequence variability was seen over the tail fibre genes, but the variability did not correlate with phage host range. The investigated T4 phages were not only species-but also strainspecific, necessitating the use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover half to two thirds of E. coli strains representing the five main pathotypes isolated from diarrhea patients.

Research paper thumbnail of Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

Nature Medicine, 2014

Metabolites from intestinal microbiota are key determinants of host-microbe mutualism and, conseq... more Metabolites from intestinal microbiota are key determinants of host-microbe mutualism and, consequently, the health or disease of the intestinal tract. However, whether such host-microbe crosstalk influences inflammation in peripheral tissues, such as the lung, is poorly understood. We found that dietary fermentable fiber content changed the composition of the gut and lung microbiota, in particular by altering the ratio of Firmicutes to Bacteroidetes. The gut microbiota metabolized the fiber, consequently increasing the concentration of circulating short-chain fatty acids (SCFAs). Mice fed a high-fiber diet had increased circulating levels of SCFAs and were protected against allergic inflammation in the lung, whereas a low-fiber diet decreased levels of SCFAs and increased allergic airway disease. Treatment of mice with the SCFA propionate led to alterations in bone marrow hematopoiesis that were characterized by enhanced generation of macrophage and dendritic cell (DC) precursors and subsequent seeding of the lungs by DCs with high phagocytic capacity but an impaired ability to promote T helper type 2 (T H 2) cell effector function. The effects of propionate on allergic inflammation were dependent on G protein-coupled receptor 41 (GPR41, also called free fatty acid receptor 3 or FFAR3), but not GPR43 (also called free fatty acid receptor 2 or FFAR2). Our results show that dietary fermentable fiber and SCFAs can shape the immunological environment in the lung and influence the severity of allergic inflammation.

Research paper thumbnail of Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli

Journal of Bacteriology, 2007

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewa... more Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene ( g23 ) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes wer...

Research paper thumbnail of Infant gut microbiota is protective against cow's milk allergy in mice despite immature ileal T-cell response

FEMS Microbiology Ecology, 2011

Faecal microbiota of healthy infant displays a large abundance of Bifidobacterium spp. and Bacter... more Faecal microbiota of healthy infant displays a large abundance of Bifidobacterium spp. and Bacteroides spp. Although some studies have reported an association between these two genera and allergy, these findings remain a subject of debate. Using a gnotobiotic mouse model of cow's milk allergy, we investigated the impact of an infant gut microbiotamainly composed of Bifidobacterium and Bacteroides spp.on immune activation and allergic manifestations. The transplanted microbiota failed to restore an ileal T-cell response similar to the one observed in conventional mice. This may be due to the low bacterial translocation into Peyer's patches in gnotobiotic mice. The allergic response was then monitored in germ-free, gnotobiotic, and conventional mice after repeated oral sensitization with whey proteins and cholera toxin. Colonized mice displayed a lower drop of rectal temperature upon oral challenge with b-lactoglobulin, lower plasma mMCP-1, and lower anti-BLG IgG1 than germ-free mice. The foxp3 gene was highly expressed in the ileum of both colonized mice that were protected against allergy. This study is the first demonstration that a transplanted healthy infant microbiota mainly composed of Bifidobacterium and Bacteroides had a protective impact on sensitization and food allergy in mice despite altered T-cell response in the ileum.

Research paper thumbnail of Phylogenetic, Functional and Safety Features of 1950s B. infantis Strains

Microorganisms, 2022

Strains of Bifidobacterium longum subsp. infantis (B. infantis) are amongst the first to colonize... more Strains of Bifidobacterium longum subsp. infantis (B. infantis) are amongst the first to colonize the infant gut, partly due to their capacity to metabolize complex human milk oligosaccharides (HMO), and are proposed to play a key role in the development of the infant gut. Since early life, B. infantis supplementation is of high interest, and detailed phylogenetic, functional and safety characterization of the selected strains should be pursued. Using a combination of long and short-read sequencing technologies, we first decipher the genetic distance between different isolates of the same B. infantis strain. Using the same approach, we show that several publicly available genomes recapitulate this strain-level distance as compared to two of the first strains obtained in the 1950s. Furthermore, we demonstrate that the two 1950s B. infantis strains display different functional and safety attributes, as ATCC 15697 is resistant to streptomycin and shows a preference towards lacto-N-tetr...

Research paper thumbnail of Dynamics of Infant Gut Microbiota Are Influenced by Delivery Mode and Gestational Duration and Are Associated with Subsequent Adiposity

mBio, 2015

We found that the relatively simple microbiota of young infants shifts predictably to a more matu... more We found that the relatively simple microbiota of young infants shifts predictably to a more mature anaerobic microbiota during infancy and the dynamics of this shift are influenced by environmental factors. In this longitudinal study of 75 infants, we demonstrate high interindividual variability within the normal range of birth outcomes, especially in the rate of microbiota progression. Most had acquired a microbiota profile high in Bifidobacterium and Collinsella by 6 months of age, but the time point of this acquisition was later in infants delivered by caesarean section and those born after a shorter duration of gestation. Independently of the delivery mode and gestation duration, infants who acquired a profile high in Bifidobacterium and Collinsella at a later age had lower adiposity at 18 months of age. IMPORTANCE This study shows that the acquisition of the early microbiota is strongly influenced by environmental factors such as the delivery mode and duration of gestation, even in healthy neonates. The composition of the early microbiota has been linked with long-lasting effects on health and disease. Here we show that the rate of acquisition of certain microbiota predicts adiposity at 18 months of age and so potentially the risk of later obesity. . 2015. Dynamics of infant gut microbiota are influenced by delivery mode and gestational duration and are associated with subsequent adiposity. mBio 6(1):e02419-14.

Research paper thumbnail of T4 phages against Escherichia coli diarrhea: Potential and problems

Virology, 2009

A combination of in vitro and in vivo experiments with comparative phage genomics was used for th... more A combination of in vitro and in vivo experiments with comparative phage genomics was used for the rational design of a phage cocktail against E. coli diarrhea. Orally applied T4 coliphages representing three different subgroups (T4-, RB49-and JS98-like phages) had no negative impact on the murine gut microbiota. T4 phages were found with high titers in the cecum and colon and lower titers in the small intestine, but were not detected in the blood, liver or spleen. No adverse effects were observed after one-month exposure to phage nor were serum anti-T4 antibodies detected. T4 phages belonging to the same subgroup showed closely related genomes that differed by 12 (phage JS10 vs. JS98 reference) to 17 (phage JSE vs. RB49 reference) insertion/deletions mostly representing single small ORFs. Bioinformatic analysis did not reveal undesired genes in the T4 genomes. Sequence variability was seen over the tail fibre genes, but the variability did not correlate with phage host range. The investigated T4 phages were not only species-but also strainspecific, necessitating the use of phage cocktails consisting of 10 and 16 T4 phage isolates to cover half to two thirds of E. coli strains representing the five main pathotypes isolated from diarrhea patients.

Research paper thumbnail of Effect of Lactobacillus rhamnosus CGMCC1.3724 supplementation on weight loss and maintenance in obese men and women

British Journal of Nutrition, 2014

The present study investigated the impact of a Lactobacillus rhamnosus CGMCC1.3724 (LPR) suppleme... more The present study investigated the impact of a Lactobacillus rhamnosus CGMCC1.3724 (LPR) supplementation on weight loss and maintenance in obese men and women over 24 weeks. In a double-blind, placebo-controlled, randomised trial, each subject consumed two capsules per d of either a placebo or a LPR formulation (1.6 × 10(8) colony-forming units of LPR/capsule with oligofructose and inulin). Each group was submitted to moderate energy restriction for the first 12 weeks followed by 12 weeks of weight maintenance. Body weight and composition were measured at baseline, at week 12 and at week 24. The intention-to-treat analysis showed that after the first 12 weeks and after 24 weeks, mean weight loss was not significantly different between the LPR and placebo groups when all the subjects were considered. However, a significant treatment × sex interaction was observed. The mean weight loss in women in the LPR group was significantly higher than that in women in the placebo group (P = 0.02) after the first 12 weeks, whereas it was similar in men in the two groups (P= 0.53). Women in the LPR group continued to lose body weight and fat mass during the weight-maintenance period, whereas opposite changes were observed in the placebo group. Changes in body weight and fat mass during the weight-maintenance period were similar in men in both the groups. LPR-induced weight loss in women was associated not only with significant reductions in fat mass and circulating leptin concentrations but also with the relative abundance of bacteria of the Lachnospiraceae family in faeces. The present study shows that the Lactobacillus rhamnosus CGMCC1.3724 formulation helps obese women to achieve sustainable weight loss.

Research paper thumbnail of Narcisse: a mirror view of conserved syntenies

Nucleic Acids Research, 2007

New methods and tools are needed to exploit the unprecedented source of information made availabl... more New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.

Research paper thumbnail of Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli

Journal of Bacteriology, 2007

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewa... more Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.