Data from: The Sphagnum microbiome supports greatly bog ecosystem functioning under extreme conditions

Sphagnum-dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem, and strongly contribute to global biosphere functioning. Sphagnum is colonised by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina-based metagenomic approach followed by de novo assembly and MG-RAST annotation. An inter-environmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic life style under poikilohydric and ombrotrophic conditions. To realise a plasticity-stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair, and self-controlling mechanisms. Multiple microbe-microbe and plant-microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR-dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio-resource for environmental biotechnology – with respect to novel enzymes or stress-protecting bacteria

4516652.3_M2norm_L008_R1_paired_de_novo_assembly_Nmetabolism

Partial gene sequences encoding for nitrogen metabolism from the normalised Sphagnum magellanicum metagenome

4533611.3_M2_retainMode_16S

Partial 16S rRNA gene sequences from the complete Sphagnum magellanicum metagenom

4533611.3_M2_retianMode_Nmetabolism

Partial gene sequences encoding for nitrogen metabolism from the complete Sphagnum magellanicum metagenome

Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils

Clinical stomach interventions, such as acid inhibition or bypass surgery, have been linked to fecal microbiota alterations. We demonstrate that the stomach microbiota largely overlaps those of adjacent gastrointestinal locations and identify gradual decreases and increases in the relative abundances of specific bacteria within the stomach, suggesting selective enrichment and depletion. Moreover, similarities between stomach and esophagus samples are proportional to the concentrations of Streptococcus (Firmicutes) in the stomach. The relative abundance of Firmicutes in the stomach, compared to that of Bacteroidetes, is increased in RNA relative to DNA, indicating higher transcriptional activity. Moreover, increased absolute bacterial loads are associated with decreased relative abundance of Firmicutes and higher relative abundance of Bacteroidetes. Our findings characterize the stomach microbiota as influenced by Bacteroidetes influx against a background of transcriptionally more active Firmicutes. Human, mouse, and gerbil stomach microbiotas differ at lower taxonomic levels, which might affect the utility of these model organisms.Clinical interventions in the stomach have been linked to fecal microbiota alterations, suggesting a function of the stomach in gastrointestinal (GI) homeostasis. We sought to determine the taxonomic bacterial biogeography of the upper GI tract, including different sites within the human stomach (cardia, corpus, and antrum), adjacent upstream (esophagus) and downstream (duodenum) locations, and luminal contents (aspirate), as well as whole-stomach samples from mice and gerbils. Qualitative and quantitative DNA- and RNA-based taxonomic microbiota analyses were combined to study the relationship of relative and absolute bacterial abundances and transcriptionally active bacterial microbiota components in the stomach of humans and mice. Stomach microbiota compositions resembled those of esophagus and duodenum. However, along the descending GI tract, the relative abundances of specific oropharyngeal commensals decreased (Streptococcus) or increased (Rothia mucilaginosa, Porphyromonas, and Lachnospiraceae). Furthermore, the compositional similarity (weighted UniFrac) between stomach aspirates and esophageal biopsy samples increased with gastric Streptococcus relative abundance. In both human aspirate and mouse stomach samples, Firmicutes were more abundant among transcriptionally active bacteria than Bacteroidetes. The relative abundance of Firmicutes in the stomach was negatively correlated and that of Bacteroidetes was positively correlated with absolute bacterial abundance, suggesting a disproportionate increase of Bacteroidetes over Firmicutes at higher bacterial densities. Human, mouse, and gerbil stomach samples showed similarities at higher taxonomic levels but differences at lower taxonomic levels. Our findings suggest selective enrichment and depletion of specific bacterial taxa in the stomach and Firmicutes being transcriptionally more active than Bacteroidetes that increase in relative abundance with total bacterial load

Impact of ITS-Based Sequencing on Antifungal Treatment of Patients with Suspected Invasive Fungal Infections

Molecular techniques including the sequencing of fungal-specific DNA targets are increasingly used in the diagnosis of suspected invasive fungal infections. In contrast to established biomarkers like galactomannan or 1-3-β-d-glucan, the clinical impact of these methods remains unknown. We retrospectively investigated the impact of ITS1-sequencing on antifungal treatment strategies in 71 patients (81 samples) with suspected invasive fungal infections. ITS-sequencing either confirmed already ongoing antifungal therapy (19/71 patients, 27%), led to a change in antifungal therapy (11/71, 15%) or supported the decision to withhold antifungal treatment (34/71, 48%) (in seven of 71 patients, ITS-sequencing results were obtained postmortem). ITS-sequencing results led to a change in antifungal therapy in a relevant proportion of patients, while it confirmed therapeutic strategies in the majority. Therefore, ITS-sequencing was a useful adjunct to other fungal diagnostic measures in our cohort

Molecular Profiling of Keratinocyte Skin Tumors Links Staphylococcus aureus Overabundance and Increased Human β-Defensin-2 Expression to Growth Promotion of Squamous Cell Carcinoma

The skin microbiota plays a prominent role in health and disease; however, its contribution to skin tumorigenesis is not well understood. We comparatively assessed the microbial community compositions from excision specimens of the main human non-melanoma skin cancers, actinic keratosis (AK), squamous cell carcinoma (SCC) and basal cell carcinoma (BCC). Keratinocyte skin tumors are characterized by significantly different microbial community compositions, wherein AK and SCC are more similar to each other than to BCC. Notably, in SCC, which represents the advanced tumor entity and frequently develops from AK, overabundance of Staphylococcus aureus, a known skin pathogen, was noted. Moreover, S. aureus overabundance was significantly associated with increased human β-defensin-2 (hBD-2) expression in SCC. By challenging human SCC cell lines with S. aureus, a specific induction of hBD-2 expression and increased tumor cell growth was seen. Increased proliferation was also induced by directly challenging SCC cells with hBD-2. Together, our data indicate that a changed microbial community composition in SCC, specified by S. aureus overabundance, might promote tumor cell growth via modulation of hBD-2 expression

Comparative overview of Genomic Islands (GIs).

<p>(<b>A</b>) VGI I (PAI) with the T4SS and putative prohage I, (<b>B</b>) VGI II with a <i>vir</i>-gene cluster and plasmid-related genes, (<b>C</b>) VGI III containing the surface array protein cluster and prohage III, (<b>D</b>) VGI IV containing the CRISPR-array and prophage IV and (<b>E</b>) FGI II with prophage-related genes (prophage II) and the CRISPR-cluster (array and <i>cas</i>-genes). The GI borders to genes shared between the subspecies (grey) are indicated with nucleotide position. Gene clusters are colored as follows: phage-related genes (orange), plasmid related genes (green), integrases and transposases (blue), T4SS (red), effector proteins (yellow), surface array proteins (purple), <i>cas</i>-genes (lavender), tRNAs (green boxes); Each x represents a hypothetical protein and their numbers in tandem are indicated above.</p

Comparative Genome Analysis of <i>Campylobacter fetus</i> Subspecies Revealed Horizontally Acquired Genetic Elements Important for Virulence and Niche Specificity

<div><p><i>Campylobacter fetus</i> are important animal and human pathogens and the two major subspecies differ strikingly in pathogenicity. <i>C. fetus</i> subsp. <i>venerealis</i> is highly niche-adapted, mainly infecting the genital tract of cattle. <i>C. fetus</i> subsp. <i>fetus</i> has a wider host-range, colonizing the genital- and intestinal-tract of animals and humans. We report the complete genomic sequence of <i>C. fetus</i> subsp. <i>venerealis</i> 84-112 and comparisons to the genome of <i>C. fetus</i> subsp. <i>fetus</i> 82-40. Functional analysis of genes predicted to be involved in <i>C. fetus</i> virulence was performed. The two subspecies are highly syntenic with 92% sequence identity but <i>C. fetus</i> subsp. <i>venerealis</i> has a larger genome and an extra-chromosomal element. Aside from apparent gene transfer agents and hypothetical proteins, the unique genes in both subspecies comprise two known functional groups: lipopolysaccharide production, and type IV secretion machineries. Analyses of lipopolysaccharide-biosynthesis genes in <i>C. fetus</i> isolates showed linkage to particular pathotypes, and mutational inactivation demonstrated their roles in regulating virulence and host range. The comparative analysis presented here broadens knowledge of the genomic basis of <i>C. fetus</i> pathogenesis and host specificity. It further highlights the importance of surface-exposed structures to <i>C. fetus</i> pathogenicity and demonstrates how evolutionary forces optimize the fitness and host-adaptation of these pathogens.</p></div