Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples

We report on Moonbase, an innovative pipeline that builds upon the established tools of MetaPhlAn and Kraken2, enhancing their capabilities for more precise taxonomic detection and quantification in diverse microbial communities. Moonbase enhances the performance of Kraken2 mapping by providing an efficient method for constructing project-specific databases. Moonbase was evaluated using synthetic metagenomic samples and compared against MetaPhlAn3 and generalized Kraken2 databases. Moonbase significantly improved species precision and quantification, outperforming marker genes and generalized databases. Construction of a phylogenetic tree from 16S genome data in Moonbase allowed for the incorporation of UniFrac-type phylogenetic information into diversity calculations of samples. We demonstrated that the resulting analysis increased statistical power in distinguishing microbial communities. This study highlights the continual evolution of metagenomic tools with the goal of improving metagenomic analysis and highlighting the potential of the Moonbase pipeline.

Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes

The vaginal microbiota refers to the microorganisms that reside in the vagina. These microorganisms contribute significantly to a woman's reproductive and general health. A healthy vaginal microbiota is typically a low-diversity environment with a predominance of lactic acid-producing Lactobacillus species. Factors such as antibiotic use, sexual activity, and hormonal changes can disrupt the balance of the vaginal microbiota, leading to conditions such as bacterial vaginosis. The composition of the vaginal microbiota changes and takes on added importance during pregnancy, serving as a barrier against infection for both mother and fetus. Despite the importance of the microorganisms that colonize the vagina, details of how changes in composition and diversity can impact pregnancy outcomes is poorly understood. This is especially true for woman with a high prevalence of Gardnerella vaginalis. Here we report on a diverse cohort of 749 women, enrolled in the InSPIRe cohort, during their final trimester of pregnancy. We show that Lactobacilli, including L. crispatus are important in maintaining low diversity, and that depletion in this critical community is linked with preterm delivery. We further demonstrate that it is overall diversity of the vaginal microbiota, not specific species, which provides the best indicator of risk.

Meet-U: Educating through research immersion

We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4–5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master’s students in bioinformatics and modeling, with protein–protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.

SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline

Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of biomolecules.

Microbialites and global environmental change across the Permian-Triassic boundary: a synthesis

Permian-Triassic boundary microbialites (PTBMs) are thin (0.05-15 m) carbonates formed after the end-Permian mass extinction. They comprise Renalcis-group calcimicrobes, microbially mediated micrite, presumed inorganic micrite, calcite cement (some may be microbially influenced) and shelly faunas. PTBMs are abundant in low-latitude shallow-marine carbonate shelves in central Tethyan continents but are rare in higher latitudes, likely inhibited by clastic supply on Pangaea margins. PTBMs occupied broadly similar environments to Late Permian reefs in Tethys, but extended into deeper waters. Late Permian reefs are also rich in microbes (and cements), so post-extinction seawater carbonate saturation was likely similar to the Late Permian. However, PTBMs lack widespread abundant inorganic carbonate cement fans, so a previous interpretation that anoxic bicarbonate-rich water upwelled to rapidly increase carbonate saturation of shallow seawater, post-extinction, is problematic. Preliminary pyrite framboid evidence shows anoxia in PTBM facies, but interbedded shelly faunas indicate oxygenated water, perhaps there was short-term pulsing of normally saturated anoxic water from the oxygen-minimum zone to surface waters. In Tethys, PTBMs show geographic variations: (i) in south China, PTBMs are mostly thrombolites in open shelf settings, largely recrystallised, with remnant structure of Renalcis-group calcimicrobes; (ii) in south Turkey, in shallow waters, stromatolites and thrombolites, lacking calcimicrobes, are interbedded, likely depth-controlled; and (iii) in the Middle East, especially Iran, stromatolites and thrombolites (calcimicrobes uncommon) occur in different sites on open shelves, where controls are unclear. Thus, PTBMs were under more complex control than previously portrayed, with local facies control playing a significant role in their structure and composition.

Seasonal variability in the gut ultrastructure of the parasitic copepod Neoergasilus japonicus (Copepoda, Poecilostomatoida)

The gut structure and ultrastructure of Neoergasilus japonicus (Harada, 1930), a copepod from the family Ergasilidae (Copepoda, Poecilostomatoida) and a parasite of fish, were compared at different periods of the life cycle: in free-living specimens in October and after attaching to fish in January and June. Differences in the depth of the intestinal epithelium were prominent and other cellular characteristics appeared seasonally variable. We relate these to changes in the physiological activity. Preliminary data from stable-isotope analyses of attached specimens suggest nutritional contribution from parasitism. The possibility of a diapause in the life cycle, as well as the relationship between the morphology of the gut and early evolutionary parasitism of N. japonicus, are discussed.

Formation of the gut in the first two naupliar stages of Acartia clausi and Hemidiaptomus roubaui (Copepoda, Calanoida): comparative structural and ultrastructural aspects

In this study, the structure and ultrastructure of the digestive system are compared in the early larval stages (nauplii I and II) of two copepod calanoid species, Acartia clausi Giesbrecht, 1889 and Hemidiaptomus roubaui Richard, 1888. The nauplii I of both species have no functional digestive tract, which is represented initially only by a blind esophageal slit and yolky endodermal cells, which fill the most part of the naupliar body, whereas at the nauplius II stage the differentiated digestive tract becomes functional. The resorption cavity corresponding to the future midgut is progressively formed in the endodermal mass during the premolt phase; it is surrounded by differentiating epithelial cells. In the ecdysial phase the foregut has associated labral glands, the midgut young R-, B-, and R'-cells of epithelium, and there is a short open hindgut.

[Treatment of neurosurgical bacterial meningitis using the combination of ceftriaxone-fosfomycin]

16 patients with bacterial meningitis following a neurosurgical procedure were given a combination of ceftriaxone and fosfomycin. 8 microorganism were isolated: 2 Staphylococcus epidermidis, 1 Staphylococcus aureus, 1 Neisseria meningitidis, 1 Streptococcus pneumoniae, 1 Haemophilus influenzae, 1 Serratia marcescens and 1 Aeromonas hydrophila. No pathogen was identified in the remaining cases. All of the isolated strains were susceptible to both antibiotics. In vitro, neither synergy nor antagonism were observed between the two antimicrobial agents. The acute infectious episode resolved in all patients. One relapse only was observed, in a patient with meningitis related to a ventricular shunt, and successfully treated by the same therapeutic schedule associated with removal of the tubing. Lastly, CSF concentrations of both antibiotics were assayed and found to be comparable with those reported by most author.