A Cenozoic-style scenario for the end-Ordovician glaciation

The end-Ordovician was an enigmatic interval in the Phanerozoic, known for massive glaciation potentially at elevated CO2 levels, biogeochemical cycle disruptions recorded as large isotope anomalies and a devastating extinction event. Ice-sheet volumes claimed to be twice those of the Last Glacial Maximum paradoxically coincided with oceans as warm as today. Here we argue that some of these remarkable claims arise from undersampling of incomplete geological sections that led to apparent temporal correlations within the relatively coarse resolution capability of Palaeozoic biochronostratigraphy. We examine exceptionally complete sedimentary records from two, low and high, palaeolatitude settings. Their correlation framework reveals a Cenozoic-style scenario including three main glacial cycles and higher-order phenomena. This necessitates revision of mechanisms for the end-Ordovician events, as the first extinction is tied to an early phase of melting, not to initial cooling, and the largest δ13C excursion occurs during final deglaciation, not at the glacial apex

Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota

The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can affect the consortium dramatically. Antibiotic cessation does not necessarily restore pre-treatment conditions and disturbed microbiota are often susceptible to pathogen invasion. Here we propose a mathematical model to explain how antibiotic-mediated switches in the microbiota composition can result from simple social interactions between antibiotic-tolerant and antibiotic-sensitive bacterial groups. We build a two-species (e.g. two functional-groups) model and identify regions of domination by antibiotic-sensitive or antibiotic-tolerant bacteria, as well as a region of multistability where domination by either group is possible. Using a new framework that we derived from statistical physics, we calculate the duration of each microbiota composition state. This is shown to depend on the balance between random fluctuations in the bacterial densities and the strength of microbial interactions. The singular value decomposition of recent metagenomic data confirms our assumption of grouping microbes as antibiotic-tolerant or antibiotic-sensitive in response to a single antibiotic. Our methodology can be extended to multiple bacterial groups and thus it provides an ecological formalism to help interpret the present surge in microbiome data.Comment: 20 pages, 5 figures accepted for publication in Plos Comp Bio. Supplementary video and information availabl

Genome Mining for Radical SAM Protein Determinants Reveals Multiple Sactibiotic-Like Gene Clusters

Thuricin CD is a two-component bacteriocin produced by Bacillus thuringiensis that kills a wide range of clinically significant Clostridium difficile. This bacteriocin has recently been characterized and consists of two distinct peptides, Trnβ and Trnα, which both possess 3 intrapeptide sulphur to α-carbon bridges and act synergistically. Indeed, thuricin CD and subtilosin A are the only antimicrobials known to possess these unusual structures and are known as the sactibiotics (sulplur to alpha carbon-containing antibiotics). Analysis of the thuricin CD-associated gene cluster revealed the presence of genes encoding two highly unusual SAM proteins (TrnC and TrnD) which are proposed to be responsible for these unusual post-translational modifications. On the basis of the frequently high conservation among enzymes responsible for the post-translational modification of specific antimicrobials, we performed an in silico screen for novel thuricin CD–like gene clusters using the TrnC and TrnD radical SAM proteins as driver sequences to perform an initial homology search against the complete non-redundant database. Fifteen novel thuricin CD–like gene clusters were identified, based on the presence of TrnC and TrnD homologues in the context of neighbouring genes encoding potential bacteriocin structural peptides. Moreover, metagenomic analysis revealed that TrnC or TrnD homologs are present in a variety of metagenomic environments, suggesting a widespread distribution of thuricin-like operons in a variety of environments. In-silico analysis of radical SAM proteins is sufficient to identify novel putative sactibiotic clusters

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

Commensal bacteria often have an especially rich source of glycan-degrading enzymes which allow them to utilize undigested carbohydrates from the food or the host. The species Ruminococcus gnavus is present in the digestive tract of ≥90% of humans and has been implicated in gut-related diseases such as inflammatory bowel diseases (IBD). Here we analysed the ability of two R. gnavus human strains, E1 and ATCC 29149, to utilize host glycans. We showed that although both strains could assimilate mucin monosaccharides, only R. gnavus ATCC 29149 was able to grow on mucin as a sole carbon source. Comparative genomic analysis of the two R. gnavus strains highlighted potential clusters and glycoside hydrolases (GHs) responsible for the breakdown and utilization of mucin-derived glycans. Transcriptomic and functional activity assays confirmed the importance of specific GH33 sialidase, and GH29 and GH95 fucosidases in the mucin utilisation pathway. Notably, we uncovered a novel pathway by which R. gnavus ATCC 29149 utilises sialic acid from sialylated substrates. Our results also demonstrated the ability of R. gnavus ATCC 29149 to produce propanol and propionate as the end products of metabolism when grown on mucin and fucosylated glycans. These new findings provide molecular insights into the strain-specificity of R. gnavus adaptation to the gut environment advancing our understanding of the role of gut commensals in health and disease

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

Recent reports have suggested the involvement of gut microbiota in the progression of colorectal cancer (CRC). We utilized pyrosequencing based analysis of 16S rRNA genes to determine the overall structure of microbiota in patients with colorectal cancer and healthy controls; we investigated microbiota of the intestinal lumen, the cancerous tissue and matched noncancerous normal tissue. Moreover, we investigated the mucosa-adherent microbial composition using rectal swab samples because the structure of the tissue-adherent bacterial community is potentially altered following bowel cleansing. Our findings indicated that the microbial structure of the intestinal lumen and cancerous tissue differed significantly. Phylotypes that enhance energy harvest from diets or perform metabolic exchange with the host were more abundant in the lumen. There were more abundant Firmicutes and less abundant Bacteroidetes and Proteobacteria in lumen. The overall microbial structures of cancerous tissue and noncancerous tissue were similar; howerer the tumor microbiota exhibited lower diversity. The structures of the intestinal lumen microbiota and mucosa-adherent microbiota were different in CRC patients compared to matched microbiota in healthy individuals. Lactobacillales was enriched in cancerous tissue, whereas Faecalibacterium was reduced. In the mucosa-adherent microbiota, Bifidobacterium, Faecalibacterium, and Blautia were reduced in CRC patients, whereas Fusobacterium, Porphyromonas, Peptostreptococcus, and Mogibacterium were enriched. In the lumen, predominant phylotypes related to metabolic disorders or metabolic exchange with the host, Erysipelotrichaceae, Prevotellaceae, and Coriobacteriaceae were increased in cancer patients. Coupled with previous reports, these results suggest that the intestinal microbiota is associated with CRC risk and that intestinal lumen microflora potentially influence CRC risk via cometabolism or metabolic exchange with the host. However, mucosa-associated microbiota potentially affects CRC risk primarily through direct interaction with the host

Obtaining and rearing of axenic and gnotoxenic rabbits. The heteroxenic rabbit: first results

International audienc

Zircon typology combined with Sm-Nd whole-rock isotope analysis to study Brioverian sediments from the Armorican Massif

The identification of source materials contributing to mature terrigenous clastic deposits is made difficult due to a lack of useful discriminant criteria. Sm-Nd isotope analysis can provide some indication of the presence of mantle-derived constituents in elastic rocks. However, since this method is based on whole-rock samples, it is only possible to obtain the averaged composition of the different source materials involved. Moreover, Sm-Nd isotope systematics can be strongly influenced by the presence of heavy minerals rich in rare earth elements and/or displaying isotopic ratios very different to the sedimentary host. In this manner, 0.1% of zircon or 0.01% of monazite from an extraneous source is sufficient to modify significatively the Sm-Nd signature of the whole-rock. The typological study of zircon populations is an extremely valuable tool, especially since this mineral is highly resistant and exhibits a morphology controlled by the physical and chemical conditions under which it crystallized. Zircons that have been reworked in a sedimentary deposit display typologies that make it possible to identify the different igneous rock-types present in the source region. Moreover the typological study can be associated with a single-grain Pb-Pb dating. This twofold approach was applied to Brioverian sedimentary rocks (Neoproterozoic III to Early Palaeozoic in age) from the Central Brittany Domain (Armorican Massif, NW France). It is proposed that these deposits inherited a major component from juvenile crustal materials (eNd(s4e) = - 1.4 to -6.31, reflecting the presence of igneous precursors with a dominantly mantle-derived origin (zircon sub-types S19, S20, S24, S25 etc.), to which was added another component of crustal anatectic affinity (zircon sub-types S2, S6, S7 etc.). Two igneous source regions are identified on the basis of the present study: the anatectic granitic massifs of the Mancellian Batholith (540 Ma), along with a coeval ignimbritic suite of end-Proterozoic/Eocambrian age, and the syn- and post-tectonic dioritic massifs (590 to 530 Ma). Apart from these main sources of elastic supply, it is very likely that sporadic contributions arose from basic to intermediate volcanic activity of mantle origin linked to the Cadomian orogeny and from the Icartian basement

Compositional affinities of volcanic fragments in sedimentary rocks using electron microprobe analysis

The identification of clasts of volcanic origin in terrigenous detrital rocks is generally based on the observation of textural criteria. In the absence of quantitative analytical data on the chemical composition of such fragments, it is often quite difficult to identify their specific origin. However, it is now possible to use a defocused microprobe beam to obtain high-precision analyses of microcrystalline elements. The application of this technique to the groundmass of various lavas shows that the distribution of certain elements varies as a function of whole-rock composition. Three ternary diagrams, using the most discriminant parameters (K20/Na20/CaO, Fe20 3/Na20 + K20/MgO and SiO2/CaO × 10/MgO x 10), are proposed for the identification of different groundmass compositions (ultrabasic, basic, intermediate, and acid). The study of reworked clastic material from the Upper Ordovician sediments of Sardinia shows that fragments of volcanic groundmass can preserve their initial geochemical characteristics. The application of this method to microcrystalline fragments contained in Proterozoic sandstones of the Armorican Massif shows that it can be an additional approach for the identification of siliciclastic source-areas