A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.

The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates.

Phylogenetic, Functional and Safety Features of 1950s Strains.

Strains of subsp. () 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, supplementation is of high interest, and detailed phylogenetic, functional and safety characterization of the selected strains should be pursued.

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

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.

Implications of Mobile Genetic Elements for Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations.

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 as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion sequences, integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018.

A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of and .

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.

Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068).

Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the Nestle Culture Collection. Here, we disclose its full 1.9-Gb genome sequence comprising one chromosome with no plasmid.

Effect of Formula Containing Lactobacillus reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section.

Objectives: 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 Lactobacillus reuteri Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM) 17938 and comparing it with that of vaginally delivered infants.

Methods: 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.

Fully Closed Genome Sequences of Five Type Strains of the Genus Cronobacter and One Cronobacter sakazakii Strain.

Cronobacteris associated with infant infections and the consumption of reconstituted infant formula. Here we sequenced and closed six genomes ofC. condimenti(T),C.

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

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.

Rate of establishing the gut microbiota in infancy has consequences for future health.

The gut of the human neonate is colonized rapidly after birth from an early sparse and highly distinct microbiota to a more adult-like and convergent state, within 1 to 3 years. The progression of colonizing bacterial species is non-random. During the first months of life several shifts commonly occur in the species prevalent in our guts.

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

Unlabelled: 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.

Nasopharyngeal microbiota in healthy children and pneumonia patients.

Our study is the first to compare the nasopharyngeal microbiota of pediatric pneumonia patients and control children by 454 pyrosequencing. A distinct microbiota was associated with different pneumonia etiologies. Viral pneumonia was associated with a high abundance of the operational taxonomic unit (OTU) corresponding to Moraxella lacunata.

Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis.

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.

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

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.

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 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.

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

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.

T4 phages against Escherichia coli diarrhea: potential and problems.

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.

Narcisse: a mirror view of conserved syntenies.

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.

Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli.

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.