Highlights d Bacterial strains may persist within family members through transfer d Bacteria adapt dispersal strategies: heredipersistent, spatiopersistent, and tenacious d Dispersal strategies correlate with genetic bottlenecks and effective population size

The composition of the plant microbiota may be altered by ecological and evolutionary changes in the host population. Seed-associated microbiota, expected to be largely vertically transferred, have the potential to coadapt with their host over generations. Strong directional selection and changes in the genetic composition of plants during domestication and cultivation may have impacted the assembly and transmission of seed-associated microbiota. Nonetheless, the effect of plant speciation and domestication on the composition of these microbes is poorly understood. Here, we have investigated the composition of bacteria and fungi associated with the wild emmer wheat (Triticum dicoccoides) and domesticated bread wheat (Triticum aestivum). We show that vertically transmitted bacteria, but not fungi, of domesticated bread wheat species T. aestivum are less diverse and more inconsistent among individual plants compared to those of the wild emmer wheat species T. dicoccoides. We propagated wheat seeds under sterile conditions to characterize the colonization of seedlings by seed-associated microbes. Hereby, we show markedly different community compositions and diversities of leaf and root colonizers of the domesticated bread wheat compared to the wild emmer wheat. By propagating the wild emmer wheat and domesticated bread wheat in two different soils, we furthermore reveal a small effect of plant genotype on microbiota assembly. Our results suggest that domestication and prolonged breeding have impacted the vertically transferred bacteria, but only to a lesser extent have affected the soil-derived microbiota of bread wheat. IMPORTANCE Genetic and physiological changes associated with plant domestication have been studied for many crop species. Still little is known about the impact of domestication on the plant-associated microbiota. In this study, we analyze the seed-associated and soil-derived bacterial and fungal microbiota of domesticated bread wheat and wild emmer wheat. We show a significant difference in the seed-associated, but not soil-derived, bacterial communities of the wheat species. Interestingly, we find less pronounced effects on the fungal communities. Overall, this study provides novel insight into the diversity of vertically transmitted microbiota of wheat and thereby contributes to our understanding of wheat as a “metaorganism.” Insight into the wheat microbiota is of fundamental importance for the development of improved crops.

Domestication has led to substantial changes in plant physiology. How this anthropogenic intervention has contributed in altering the wheat microbiota is not well understood. Here, we investigated the role of ecological selection, drift, and dispersal in shaping the bacterial and fungal communities associated with domesticated wheat Triticum aestivum and two wild relatives, T. boeoticum and T. urartu. Our study shows that the bacterial and fungal microbiota of wild and domesticated wheat species follow distinct community assembly patterns. Further, we revealed a more prominent role of neutral processes in the assembly of the microbiota of domesticated wheat and propose that domestication has relaxed selective processes in the assembly of the wheat microbiota. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

26Plants constitute an ecological niche for microbial communities that colonize different 27 plant tissues and explore the plant habitat for reproduction and dispersal. The 28 association of microbiota and plant may be altered by ecological and evolutionary 29 changes in the host population. Seedborne microbiota, expected to be largely vertically-30 transferred, have the potential to co-adapt with their host over generations. Reduced 31 host diversity because of strong directional selection and polyploidization during plant 32 domestication and cultivation may have impacted the assembly and transmission of 33 seed-associated microbiota. Nonetheless, the effect of plant domestication on the 34 diversity of their associated microbes is poorly understood. Here we show that microbial 35 communities in domesticated wheat, Triticum aestivum, are less diverse but more 36 inconsistent among individual plants compared to the wild wheat species, T. 37 dicoccoides. We found that diversity of microbes in seeds overall is low, but comparable 38 in different wheat species, independent of their genetic and geographic origin. 39However, the diversity of seedborne microbiota that colonize the roots and leaves of 40 the young seedling is significantly reduced in domesticated wheat genotypes. Moreover, 41we observe a higher variability between replicates of T. aestivum suggesting a stronger 42 effect of chance events in microbial colonization and assembly. We also propagated wild 43 and domesticated wheat in two different soils and found that different factors govern 44 the assembly of soil-derived and seedborne microbial communities. Overall, our results 45 demonstrate that the role of stochastic processes in seedborne microbial community 46 assembly is larger in domesticated wheat compared to the wild wheat. We suggest that 47 the directional selection on the plant host and polyploidization events during 48 domestication may have decreased the degree of wheat-microbiota interactions and 49 consequently led to a decreased stable core microbiota. 50 51

Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high-throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon-specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria, and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one amongst the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths, and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems, and particular attributes of thirty-one amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.

Plant domestication has led to substantial changes in the host physiology. How this anthropogenic intervention has contributed in altering the wheat microbiota is not well understood. Here, we investigated the role of ecological selection, drift and dispersal in shaping the bacterial and fungal communities associated with domesticated wheat Triticum aestivum and two wild relatives, Triticum boeoticum and Triticum urartu. Our study shows that the bacterial and fungal microbiota of wild and domesticated wheat species follow distinct community assembly patterns. Further, we revealed a more prominent role of neutral processes in the assembly of the microbiota of domesticated wheat and propose that domestication has relaxed selective processes in the assembly of the wheat microbiota.

BackgroundSynchronous multifocal tumours are commonly observed in urothelial carcinomas of the bladder. The origin of these physically independent tumours has been proposed to occur by either intraluminal migration (clonal) or spontaneous transformation of multiple cells by carcinogens (field effect). It is unclear which model is correct, with several studies supporting both hypotheses. A potential cause of this uncertainty may be the small number of genetic mutations previously used to quantify the relationship between these tumours.MethodsTo better understand the genetic lineage of these tumours we conducted exome sequencing of synchronous multifocal pTa urothelial bladder cancers at a high depth, using multiple samples from three patients.ResultsPhylogenetic analysis of high confidence single nucleotide variants (SNV) demonstrated that the sequenced multifocal bladder cancers arose from a clonal origin in all three patients (bootstrap value 100 %). Interestingly, in two patients the most common type of tumour-associated SNVs were cytosine mutations of TpC* dinucleotides (Fisher’s exact test p < 10−41), likely caused by APOBEC-mediated deamination. Incorporating these results into our clonal model, we found that TpC* type mutations occurred 2-5× more often among SNVs on the ancestral branches than in the more recent private branches (p < 10−4) suggesting that TpC* mutations largely occurred early in the development of the tumour.ConclusionsThese results demonstrate that synchronous multifocal bladder cancers frequently arise from a clonal origin. Our data also suggests that APOBEC-mediated mutations occur early in the development of the tumour and may be a driver of tumourigenesis in non-muscle invasive urothelial bladder cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-015-1859-8) contains supplementary material, which is available to authorized users.