Although bacteria are continually acquired over the lifetime of an individual, the phylogenetic relationships of great ape species is mirrored in the compositions of their gut microbial communities.

Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.

Type VI secretion system (T6SS) is a macromolecular machine used by many Gram-negative bacteria to inject effectors/toxins into eukaryotic hosts or prokaryotic competitors for survival and fitness. To date, our knowledge of the molecular determinants and mechanisms underlying the transport of these effectors remains limited. Here, we report that two T6SS encoded valine-glycine repeat protein G (VgrG) paralogs in Agrobacterium tumefaciens C58 specifically control the secretion and interbacterial competition activity of the type VI DNase toxins Tde1 and Tde2. Deletion and domain-swapping analysis identified that the C-terminal extension of VgrG1 specifically confers Tde1 secretion and Tde1-dependent interbacterial competition activity in planta, and the C-terminal variable region of VgrG2 governs this specificity for Tde2. Functional studies of VgrG1 and VgrG2 variants with stepwise deletion of the C terminus revealed that the C-terminal 31 aa (C31) of VgrG1 and 8 aa (C8) of VgrG2 are the molecular determinants specifically required for delivery of each cognate Tde toxin. Further in-depth studies on Tde toxin delivery mechanisms revealed that VgrG1 interacts with the adaptor/chaperone-effector complex (Tap-1-Tde1) in the absence of proline-alanine-alanine-arginine (PAAR) and the VgrG1-PAAR complex forms independent of Tap-1 and Tde1. Importantly, we identified the regions involved in these interactions. Although the entire C31 segment is required for binding with the Tap-1-Tde1 complex, only the first 15 aa of this region are necessary for PAAR binding. These results suggest that the VgrG1 C terminus interacts sequentially or simultaneously with the Tap-1-Tde1 complex and PAAR to govern Tde1 translocation across bacterial membranes and delivery into target cells for antibacterial activity.type VI secretion system | VgrG | DNase effector | interbacterial competition | Agrobacterium tumefaciens

Purpose The purpose of this study is to identify the factors that influence the development of service robots, and to apply a service innovation strategic mindset to the hotel industry in Taiwan. Design/methodology/approach A mixed-methods approach, combining an expert panel and semi-structured interviews using a SMART SWOT ranking survey, was applied to understand the perspectives of hotel owners and robotics experts. Findings Fifty-three items were collected regarding the demand side of the hospitality market, showing that the Taiwan hospitality industry has good potential to implement service robots. Sixty-one items on the supply side of business were collected, showing that this robotics service can help hotels handle seasonal employment and labor utilization. The SWOT analysis identifies “The fun and curiosity aroused in consumers can enhance the promotion of service robots”, “Lack of talent in system integration”, “Taiwan’s aging society can increase the demand for service robots” and “China and South-east countries have aggressively poached talent in the global robotics market” as key issues. Originality/value Few studies have investigated robotics service for hotels using the six-dimensional service innovation model. This model helps identify six factors and implies that this new service concept can position hotels to better compete by using IT and relationship marketing strategies.

Elevated levels of genetic drift are hypothesized to be a dominant factor that influences genome size evolution across all life-forms. However, increased levels of drift appear to be correlated with genome expansion in eukaryotes but with genome contraction in bacteria, suggesting that these two groups of organisms experience vastly different mutational inputs and selective constraints. To determine the contribution of small insertion and deletion events to the differences in genome organization between eukaryotes and prokaryotes, we systematically surveyed 17 taxonomic groups across the three domains of life. Based on over 5,000 indel events in noncoding regions, we found that deletional events outnumbered insertions in all groups examined. The extent of deletional bias, when measured by the total length of insertions to deletions, revealed a marked disparity between eukaryotes and prokaryotes, whereas the ratio was close to one in the three eukaryotic groups examined, deletions outweighed insertions by at least a factor of 10 in most prokaryotes. Moreover, the strength of deletional bias is associated with the proportion of coding regions in prokaryotic genomes. Considering that genetic drift is a stochastic process and does not discriminate the exact nature of mutations, the degree of bias toward deletions provides an explanation to the differential responses of eukaryotes and prokaryotes to elevated levels of drift. Furthermore, deletional bias, rather than natural selection, is the primary mechanism by which the compact gene packing within most prokaryotic genomes is maintained.

BackgroundThe genus Spiroplasma contains a group of helical, motile, and wall-less bacteria in the class Mollicutes. Similar to other members of this class, such as the animal-pathogenic Mycoplasma and the plant-pathogenic ‘Candidatus Phytoplasma’, all characterized Spiroplasma species were found to be associated with eukaryotic hosts. While most of the Spiroplasma species appeared to be harmless commensals of insects, a small number of species have evolved pathogenicity toward various arthropods and plants. In this study, we isolated a novel strain of honeybee-associated S. melliferum and investigated its genetic composition and evolutionary history by whole-genome shotgun sequencing and comparative analysis with other Mollicutes genomes.ResultsThe whole-genome shotgun sequencing of S. melliferum IPMB4A produced a draft assembly that was ~1.1 Mb in size and covered ~80% of the chromosome. Similar to other Spiroplasma genomes that have been studied to date, we found that this genome contains abundant repetitive sequences that originated from plectrovirus insertions. These phage fragments represented a major obstacle in obtaining a complete genome sequence of Spiroplasma with the current sequencing technology. Comparative analysis of S. melliferum IPMB4A with other Spiroplasma genomes revealed that these phages may have facilitated extensive genome rearrangements in these bacteria and contributed to horizontal gene transfers that led to species-specific adaptation to different eukaryotic hosts. In addition, comparison of gene content with other Mollicutes suggested that the common ancestor of the SEM (Spiroplasma, Entomoplasma, and Mycoplasma) clade may have had a relatively large genome and flexible metabolic capacity; the extremely reduced genomes of present day Mycoplasma and ‘Candidatus Phytoplasma’ species are likely to be the result of independent gene losses in these lineages.ConclusionsThe findings in this study highlighted the significance of phage insertions and horizontal gene transfer in the evolution of bacterial genomes and acquisition of pathogenicity. Furthermore, the inclusion of Spiroplasma in comparative analysis has improved our understanding of genome evolution in Mollicutes. Future improvements in the taxon sampling of available genome sequences in this group are required to provide further insights into the evolution of these important pathogens of humans, animals, and plants.

Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events. It is possible, however, for disrupted genes to generate products that are deleterious due either to the energetic costs of their transcription and translation or to the formation of toxic proteins. We found that after their initial formation, the youngest pseudogenes in Salmonella genomes have a very high likelihood of being removed by deletional processes and are eliminated too rapidly to be governed by a strictly neutral model of stochastic loss. Those few highly degraded pseudogenes that have persisted in Salmonella genomes correspond to genes with low expression levels and low connectivity in gene networks, such that their inactivation and any initial deleterious effects associated with their inactivation are buffered. Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection.

Background: Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating.