Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes a sharp decrease in the taxonomic richness of the microbiota due to the loss of rare taxa (p = 2.06e-9), although the number of core genera shared by all infants increases substantially. Moreover, although the gut microbial succession is not strictly deterministic, we detect an overarching directionality of change through time towards the taxonomic and functional composition of the maternal microbiota. Succession is however not complete by the one year mark, as significant differences remain between one-year-olds and their mothers in terms of taxonomic (p = 0.009) and functional (p = 0.004) microbiota composition, and in taxonomic richness (p = 2.76e-37) and diversity (p = 0.016). Our results also indicate that the taxonomic composition of the microbiota shapes its functional capacities. Therefore, the observed inter-individual variability in taxonomic composition during succession is not fully compensated by functional equivalence among bacterial genera and may have important physiological consequences. Finally, network analyses suggest that positive interactions among core genera during community assembly contribute to ensure their permanence within the gut, and highlight an expansion of complexity in the interactions network as the core of taxa shared by all infants grows following the introduction of solid foods. © 2014 Vallès et al.This work has been supported by the Spanish MICINN (project SAF2009-13032-C02-02 and project CSD2009-00006 of the CONSOLIDER program). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer Reviewe

Starkeya nomas sp. nov., a prosthecate and budding bacterium isolated from an immunocompromized patient

Strain HF14-78462T is an environmental bacterium found in clinical samples from an immunocompromized patient in 2014 at Hospital Universitari i Politècnic La Fe (Valencia, Spain). Phenotypically, strain HF14-78462T cells were Gram-stain-negative, aerobic, non-spore forming and non-motile small rods which formed mucous and whitish-translucent colonies when incubated at 20-36 °C. Phylogenetic analyses based on the 16S rRNA genes and the whole genomes of closest sequenced relatives confirmed that strain HF14-78462T is affiliated with the genus Starkeya. The strain was oxidase, catalase and urease positive; but indole, lysine decarboxylase, ornithine decarboxylase and DNase negative, did not produce H2S and was able to utilize a wide variety of carbon sources including acetamide, adonitol, amygdalin, l-arabinose, citric acid, glucose, mannitol and melibiose. Unlike Starkeya novella and Starkeya koreensis, strain HF14-78462T failed to grow in thiosulphate-oxidizing media and had a narrower temperature growth range. Its genome was characterized by a size of 4.83 Mbp and a C+G content of 67.75 mol%. Major fatty acids were C18:1 ω7c, cyclo C19 : 0 and C16 : 0, its polar acids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an aminophospholipid; while the ubiquinones were Q9 (1.8 %) and Q10 (98.2 %). Digital DNA-DNA hybridization values were 41 and 41.4 against S. novella and S. koreensis, respectively, while average nucleotide identity values were around 84 %. Phenotypic, average nucleotide identity and phylogenomic comparative studies suggest that strain HF14-78462T is a new representative of the genus Starkeya and the name Starkeya nomas sp. nov. is proposed. The type strain is HF14-78462T (=CECT 30124T=LMG 31874T).Financial support was obtained by the IIS project 2013/0437.S

Differential Effects of Antibiotic Therapy on the Structure and Function of Human Gut Microbiota

The human intestinal microbiota performs many essential functions for the host. Antimicrobial agents, such as antibiotics (AB), are also known to disturb microbial community equilibrium, thereby having an impact on human physiology. While an increasing number of studies investigate the effects of AB usage on changes in human gut microbiota biodiversity, its functional effects are still poorly understood. We performed a follow-up study to explore the effect of ABs with different modes of action on human gut microbiota composition and function. Four individuals were treated with different antibiotics and samples were taken before, during and after the AB course for all of them. Changes in the total and in the active (growing) microbiota as well as the functional changes were addressed by 16S rRNA gene and metagenomic 454-based pyrosequencing approaches. We have found that the class of antibiotic, particularly its antimicrobial effect and mode of action, played an important role in modulating the gut microbiota composition and function. Furthermore, analysis of the resistome suggested that oscillatory dynamics are not only due to antibiotic-target resistance, but also to fluctuations in the surviving bacterial community. Our results indicated that the effect of AB on the human gut microbiota relates to the interaction of several factors, principally the properties of the antimicrobial agent, and the structure, functions and resistance genes of the microbial community

An aminophenothiazine inhibitor of the NCS-1/Ric8a complex regulates synaptic function in Fragile X Syndrome

2 pags. -- 31st European Crystallographic Meeting, Oviedo, Spain 22-27 Augus

Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

<div><p>In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes a sharp decrease in the taxonomic richness of the microbiota due to the loss of rare taxa (p = 2.06e-9), although the number of core genera shared by all infants increases substantially. Moreover, although the gut microbial succession is not strictly deterministic, we detect an overarching directionality of change through time towards the taxonomic and functional composition of the maternal microbiota. Succession is however not complete by the one year mark, as significant differences remain between one-year-olds and their mothers in terms of taxonomic (p = 0.009) and functional (p = 0.004) microbiota composition, and in taxonomic richness (p = 2.76e-37) and diversity (p = 0.016). Our results also indicate that the taxonomic composition of the microbiota shapes its functional capacities. Therefore, the observed inter-individual variability in taxonomic composition during succession is not fully compensated by functional equivalence among bacterial genera and may have important physiological consequences. Finally, network analyses suggest that positive interactions among core genera during community assembly contribute to ensure their permanence within the gut, and highlight an expansion of complexity in the interactions network as the core of taxa shared by all infants grows following the introduction of solid foods.</p></div

Dendrogram showing six main groups of gut microbiota genera based on functional profile clustering.

<p>Functional profiles were defined as the relative abundances of TIGRFAM subroles in a given genus. Only genera present in any sample at >1% abundance and having genes representing at least 50% of the 108 subroles detected in our complete data set were included. Clustering was based on the complete linkage method applied to a matrix of pairwise Bray-Curtis distances between the functional profiles of genera. Branches in the resulting dendrogram were collapsed when genera on the tips pertained to the same order. Orders of the same phylum have different shades of the same color.</p

Timecore Venn diagrams.

<p>Changes in the core sets of genera (A) or functions (B) present at each infant timepoint. In both cases, areas representing the different timecores are enclosed by lines of the corresponding colors. The red central circles represent the genera or functions present in all five infant timecores; areas filled in dark orange, medium orange, light orange and yellow represent features present in four, three, two or one infant timecores. The number of features included in each section of the diagram is shown and areas are approximately proportional to these numbers.</p

Heatmaps and clustering of individual gut microbiota samples for taxonomic (A) and functional composition (B).

<p>Clustering was based on Bray-Curtis distances. (A) Only the genera above 1% abundance in at least one sample are depicted. (B) Functional composition was established based on TIGRFAM main functional roles. Each sample is identified at the bottom of the heatmaps by a code that specifies the MIP to which it belongs and the corresponding timepoint. Maternal samples are additionally highlighted by means of black bars. Colors on top of each heatmap represent the timepoints to which samples belong. Pink circles identify specific clusters referred to in the text.</p

Information regarding mothers and infants obtained from questionnaires answered by the infants' parents.

<p>MIP: Mother Infant Pair.</p>a<p>For MA samples we report whether antibiotics were given during childbirth and the specific antibiotic given. In the case of C-sections, we report administration of amoxicillin, which is the standard practice in Spanish hospitals. None of the mothers had taken antibiotics before childbirth for at least three months.</p>b<p>Oftalmowell is a combination of gramicidin, neomycin and polymyxin B.</p

ANOSIM comparison of timepoints.

<p>Overall analyses for taxonomic (A) and functional (B) Bray-Curtis distances among all samples. The length of the bows indicates the level of heterogeneity and the width the number of compared samples. Statistically significant differences among timepoints are detected for both taxonomic and functional data. Note the decrease in heterogeneity with time in infants and the larger heterogeneity in MA compared to MB samples. (C) Representation of pairwise ANOSIM analyses between timepoints. Each timepoint is represented by a color and is linked by lines of this color to all timepoints from which it is not significantly different. For functional composition, significant differences appear between timepoints that are more separated in time, indicating directionality along infant development, but no such pattern is detected at the taxonomic level.</p