Heterochronic faecal transplantation boosts gut germinal centres in aged mice

Ageing is a complex multifactorial process associated with a plethora of disorders, which contribute significantly to morbidity worldwide. One of the organs significantly affected by age is the gut. Age-dependent changes of the gut-associated microbiome have been linked to increased frailty and systemic inflammation. This change in microbial composition with age occurs in parallel with a decline in function of the gut immune system, however it is not clear if there is a causal link between the two. Here we report that the defective germinal centre reaction in Peyer’s patches of aged mice can be rescued by faecal transfers from younger adults into aged mice and by immunisations with cholera toxin, without affecting germinal centre reactions in peripheral lymph nodes. This demonstrates that the poor germinal centre reaction in aged animals is not irreversible, and that it is possible to improve this response in older individuals by providing appropriate stimuli

Trace elements in size-segregated urban aerosol in relation to the anthropogenic emission sources and the resuspension

Size segregated particulate samples of atmospheric aerosols in urban site of continental part of Balkans were collected during 6 months in 2008. Six stages impactor in the size ranges: Dp ≤ 0.49 μm, 0.49 < Dp ≤ 0.95 μm, 0.95 < Dp ≤ 1.5 μm, 1.5 < Dp ≤ 3.0 μm, 3.0 < Dp ≤ 7.2 μm, and 7.2 < Dp ≤ 10.0 μm was applied for sampling. ICP-MS was used to quantify elements: Al, As, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, K, Li, Na, Ni, Mg, Mn, Pb, Sb, V, and Zn. Two main groups of elements were investigated: (1) K, V, Ni, Zn, Pb, As, and Cd with high domination in nuclei mode indicating the combustion processes as a dominant sources and (2) Al, Fe, Ca, Mg, Na, Cr, Ga, Co, and Li in coarse mode indicating mechanical processes as their main origin. The strictly crustal origin is for Mg, Fe, Ca, and Co while for As, Cd, K, V, Ni, Cu, Pb, and Zn dominates the anthropogenic influence. The PCA analysis has shown that main contribution is of resuspension (PC1, σ2 ≈ 30 %) followed by traffic (PC2, σ2 ≈ 20 %) that are together contributing around 50 % of elements in the investigated urban aerosol. The EF model shows that major origin of Cd, K, V, Ni, Cu, Pb, Zn, and As in the fine mode is from the anthropogenic sources while increase of their contents in the coarse particles indicates their deposition from the atmosphere and soil contamination. This approach is useful for the assessment of the local resuspension influence on element’s contents in the aerosol and also for the evaluation of the historical pollution of soil caused by deposition of metals from the atmosphere

MULTIMODAL SIZE SPECTRA OF SUBMICROMETER PARTICLES BEARING VARIOUS ELEMENTS IN RURAL AIR

Samples of size-segregated submicrometer aerosol particles were collected with a microorifice impactor near Deep Creek Lake, a recreational area in rural western Maryland, and analyzed for up to 44 elements by instrumental neutron activation and X-ray fluorescence analyses. Differential concentration vs particle size spectra revealed as many as four distinct submicrometer aerosol modes with diameters between 0.09 and 1.0-mu-m in a single sample. The spectra of many elements, including Al, Zn, Na, K, Br, Ca, Ga, Fe, La, Sb, Ce, Ti, and I contained two or more modes. Modal diameters and S/Se ratios for samples influenced by northeasterly winds were smaller than those influenced by westerly winds, suggesting a greater age for the latter, despite the close proximity of several large coal-fired power plants to the west of the site. Large peaks in the spectra of S, As, Se, Sb, and V occurred at mass median aerodynamic diameters ranging from 0.3 to 0.6-mu-m in both day and nighttime samples. Simple dispersion estimates suggest that large peaks observed in daytime samples must include material from multiple sources, whereas mass in those observed in nighttime samples could be accounted for by single sources

New multi-scale perspectives on the stromatolites of Shark Bay, Western Australia

A recent field-intensive program in Shark Bay, Western Australia provides new multi-scale perspectives on the world’s most extensive modern stromatolite system. Mapping revealed a unique geographic distribution of morphologically distinct stromatolite structures, many of them previously undocumented. These distinctive structures combined with characteristic shelf physiography define eight ‘Stromatolite Provinces’. Morphological and molecular studies of microbial mat composition resulted in a revised growth model where coccoid cyanobacteria predominate in mat communities forming lithified discrete stromatolite buildups. This contradicts traditional views that stromatolites with the best lamination in Hamelin Pool are formed by filamentous cyanobacterial mats. Finally, analysis of internal fabrics of stromatolites revealed pervasive precipitation of microcrystalline carbonate (i.e. micrite) in microbial mats forming framework and cement that may be analogous to the micritic microstructures typical of Precambrian stromatolites. These discoveries represent fundamental advances in our knowledge of the Shark Bay microbial system, laying a foundation for detailed studies of stromatolite morphogenesis that will advance our understanding of benthic ecosystems on the early Earth

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

BACKGROUND: A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. RESULTS: Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. CONCLUSIONS: This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-016-0224-8) contains supplementary material, which is available to authorized users