Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria

The intestinal ecosystem is formed by a complex, yet highly characteristic microbial community. The parameters defining whether this community permits invasion of a new bacterial species are unclear. In particular, inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance) is poorly understood. To analyze the mechanisms of microbiota-mediated protection from Salmonella enterica induced enterocolitis, we used a mouse infection model and large scale high-throughput pyrosequencing. In contrast to conventional mice (CON), mice with a gut microbiota of low complexity (LCM) were highly susceptible to S. enterica induced colonization and enterocolitis. Colonization resistance was partially restored in LCM-animals by co-housing with conventional mice for 21 days (LCM(con21)). 16S rRNA sequence analysis comparing LCM, LCM(con21) and CON gut microbiota revealed that gut microbiota complexity increased upon conventionalization and correlated with increased resistance to S. enterica infection. Comparative microbiota analysis of mice with varying degrees of colonization resistance allowed us to identify intestinal ecosystem characteristics associated with susceptibility to S. enterica infection. Moreover, this system enabled us to gain further insights into the general principles of gut ecosystem invasion by non-pathogenic, commensal bacteria. Mice harboring high commensal E. coli densities were more susceptible to S. enterica induced gut inflammation. Similarly, mice with high titers of Lactobacilli were more efficiently colonized by a commensal Lactobacillus reuteri(RR) strain after oral inoculation. Upon examination of 16S rRNA sequence data from 9 CON mice we found that closely related phylotypes generally display significantly correlated abundances (co-occurrence), more so than distantly related phylotypes. Thus, in essence, the presence of closely related species can increase the chance of invasion of newly incoming species into the gut ecosystem. We provide evidence that this principle might be of general validity for invasion of bacteria in preformed gut ecosystems. This might be of relevance for human enteropathogen infections as well as therapeutic use of probiotic commensal bacteria.

Determinants of Acidobacteria activity inferred from the relative abundances of 16S rRNA transcripts in German grassland and forest soils

16S rRNA genes and transcripts of Acidobacteria were investigated in 57 grassland and forest soils of three different geographic regions. Acidobacteria contributed 9-31% of bacterial 16S rRNA genes whereas the relative abundances of the respective transcripts were 4-16%. The specific cellular 16S rRNA content (determined as molar ratio of rRNA:rRNA genes) ranged between 3 and 80, indicating a low in situ growth rate. Correlations with flagellate numbers, vascular plant diversity and soil respiration suggest that biotic interactions are important determinants of Acidobacteria 16S rRNA transcript abundances in soils. While the phylogenetic composition of Acidobacteria differed significantly between grassland and forest soils, high throughput denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism fingerprinting detected 16S rRNA transcripts of most phylotypes in situ. Partial least squares regression suggested that chemical soil conditions such as pH, total nitrogen, C:N ratio, ammonia concentrations and total phosphorus affect the composition of this active fraction of Acidobacteria. Transcript abundance for individual Acidobacteria phylotypes was found to correlate with particular physicochemical (pH, temperature, nitrogen or phosphorus) and, most notably, biological parameters (respiration rates, abundances of ciliates or amoebae, vascular plant diversity), providing culture-independent evidence for a distinct niche specialization of different Acidobacteria even from the same subdivision.

Debris discs around M stars: non-existence versus non-detection

Motivated by the reported dearth of debris discs around M stars, we use survival models to study the occurrence of planetesimal discs around them. These survival models describe a planetesimal disc with a small number of parameters, determine if it may survive a series of dynamical processes and compute the associated infrared excess. For the Wide-field Infrared Survey Explorer (WISE) satellite, we demonstrate that the dearth of debris discs around M stars may be attributed to the small semimajor axes generally probed if either: (1) the dust grains behave like blackbodies emitting at a peak wavelength coincident with the observed one; (2) or the grains are hotter than predicted by their blackbody temperatures and emit at peak wavelengths that are shorter than the observed one. At these small distances from the M star, planetesimals are unlikely to survive or persist for time-scales of 300 Myr or longer if the disc is too massive. Conversely, our survival models allow for the existence of a large population of low-mass debris discs that are too faint to be detected with current instruments. We gain further confidence in our interpretation by demonstrating the ability to compute infrared excesses for Sun-like stars that are broadly consistent with reported values in the literature. However, our interpretation becomes less clear and large infrared excesses are allowed if only one of these scenarios holds: (3) the dust grains are hotter than blackbody and predominantly emit at the observed wavelength; (4) or are blackbody in nature and emit at peak wavelengths longer than the observed one. Both scenarios imply that the parent planetesimals reside at larger distances from the star than inferred if the dust grains behaved like blackbodies. In all scenarios, we show that the infrared excesses detected at 22 μm (via WISE) and 70 μm (via Spitzer) from AU Mic are easily reconciled with its young age (12 Myr). Conversely, the existence of the old debris disc (2–8 Gyr) from GJ 581 is due to the large semimajor axes probed by the Herschel PACS instrument. We elucidate the conditions under which stellar wind drag may be neglected when considering dust populations around M stars. The WISE satellite should be capable of detecting debris discs around young M stars with ages ∼10 Myr.