Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.

BackgroundNucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as transcription, genetic instability, DNA repair, DNA replication, epigenetic mechanisms, regulation of translation, and alternative splicing. G-quadruplexes play important roles in human diseases and are being considered as targets for a variety of therapies. Identification of functional G-quadruplexes and the study of their overall distribution in genomes and transcriptomes is an important pursuit. Traditional computational methods map sequence motifs capable of forming G-quadruplexes but have difficulty in distinguishing motifs that occur by chance from ones which fold into G-quadruplexes.ResultsWe present Quadruplex forming ‘G’-rich sequences (QGRS)-Conserve, a computational method for calculating motif conservation across exomes and supports filtering to provide researchers with more precise methods of studying G-quadruplex distribution patterns. Our method quantitatively evaluates conservation between quadruplexes found in homologous nucleotide sequences based on several motif structural characteristics. QGRS-Conserve also efficiently manages overlapping G-quadruplex sequences such that the resulting datasets can be analyzed effectively.ConclusionsWe have applied QGRS-Conserve to identify a large number of G-quadruplex motifs in the human exome conserved across several mammalian and non-mammalian species. We have successfully identified multiple homologs of many previously published G-quadruplexes that play post-transcriptional regulatory roles in human genes. Preliminary large-scale analysis identified many homologous G-quadruplexes in the 5′- and 3′-untranslated regions of mammalian species. An expectedly smaller set of G-quadruplex motifs was found to be conserved across larger phylogenetic distances. QGRS-Conserve provides means to build datasets that can be filtered and categorized in a variety of biological dimensions for more targeted studies in order to better understand the roles that G-quadruplexes play.

Many microbial functions happen within communities of interacting species. Explaining how species with intrinsically disparate fitness can coexist is important for applications such as manipulating hostassociated microbiota or engineering industrial communities. Previous coexistence studies have often neglected interaction mechanisms. Here, we formulate and experimentally constrain a model in which chemical mediators of microbial interactions (e.g. metabolites or waste-products) are explicitly incorporated. We construct many instances of coexistence by simulating community assembly through enrichment and ask how species interactions can explain coexistence. We show that growth-facilitating influences between members are favored in assembled communities. Among negative influences, selfrestraint, such as production of self-inhibiting waste, contributes to coexistence, whereas inhibition of other species disrupts coexistence. Coexistence is also favored when interactions are mediated by depletable chemicals that get consumed or degraded, rather than by reusable chemicals that are unaffected by recipients. Our model creates null predictions for coexistence driven by chemicalmediated interactions.

In comparison to protein coding sequences, the impact of mutation and natural selection on the sequence and function of non-coding (ncRNA) genes is not well understood. Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be rapidly evolving. Compared to protein coding sequences, there are many challenges associated with assessment of ncRNAs that are not well addressed by conventional phylogenetic approaches, including: short sequence length, lack of primary sequence conservation, and the importance of secondary structure for biological function. Riboswitches are structured ncRNAs that directly interact with small molecules to regulate gene expression in bacteria. They typically consist of a ligand-binding domain (aptamer) whose folding changes drive changes in gene expression. The glycine riboswitch is among the most well-studied due to the widespread occurrence of a tandem aptamer arrangement (tandem), wherein two homologous aptamers interact with glycine and each other to regulate gene expression. However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton). Here we use graph clustering to circumvent the limitations of traditional phylogenetic analysis when studying the relationship between the tandem and singleton glycine aptamers. Graph clustering enables a broader range of pairwise comparison measures to be used to assess aptamer similarity. Using this approach, we show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved, and that which aptamer is conserved depends on the regulated gene. Furthermore, our analysis also reveals that singleton aptamers are more similar to either the first or second tandem aptamer, again based on the regulated gene. Taken together, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with the regulated gene(s) dictating which glycine-binding aptamer is conserved.

Aims This study was performed to evaluate the efficacy of butanoic acid against bacterial pathogens including Acinetobacter baumannii and Staphylococcus pseudintermedius. Methods and Results Vegetative bacteria were exposed to butanoic acid in vitro and log reduction was quantified using viable count assays. The maximum (8 and 9) log inactivation was determined by qualitatively assaying for growth/no‐growth after a 48‐h incubation (37°C). Membrane integrity after exposure to butanoic acid was determined by propidium iodide staining, scanning electron microscopy, membrane depolarization and inductively coupled plasma analysis. Cytosolic pH was measured by 5‐(6‐)carboxyfluorescein succinimidyl ester. Conclusions Inhibitory concentrations of butanoic acid ranged between 11 and 21 mmol l−1 for Gram‐positive and Gram‐negative species tested. The maximum log reduction of A. baumannii was achieved with a 10‐s exposure of 0·50 mol l−1 of butanoic acid. Staphylococcus pseudintermedius required 0·40 mol l−1 of butanoic acid to achieve the same level of reduction in the same time period. Inactivation was associated with membrane permeability and acidification of the cytosol. Significance and Impact of the Study Antibiotic resistance among bacterial pathogens necessitates the utilization of novel therapeutics for disinfection and biological control. These results may facilitate the development of butanoic acid as an effective agent against a broad‐spectrum of antibiotic‐resistant bacterial pathogens.

24In comparison to protein coding sequences, the impact of mutation and natural selection 25 on the sequence and function of non-coding (ncRNA) genes is not well understood. 26Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be 27 rapidly evolving. Compared to protein coding sequences, there are many challenges 28 associated with assessment of ncRNAs that are not well addressed by conventional 29 phylogenetic approaches, including: short sequence length, lack of primary sequence 30 conservation, and the importance of secondary structure for biological function. 31Riboswitches are structured ncRNAs that directly interact with small molecules to 32 regulate gene expression in bacteria. They typically consist of a ligand-binding domain 33 (aptamer) whose folding changes drive changes in gene expression. The glycine 34 riboswitch is among the most well-studied due to the widespread occurrence of a 35 tandem aptamer arrangement (tandem), wherein two homologous aptamers interact 36 with glycine and each other to regulate gene expression. However, a significant 37 proportion of glycine riboswitches are comprised of single aptamers (singleton). Here 38 we use graph clustering to circumvent the limitations of traditional phylogenetic analysis 39 when studying the relationship between the tandem and singleton glycine aptamers. 40Graph clustering enables a broader range of pairwise comparison measures to be used 41 to assess aptamer similarity. Using this approach, we show that one aptamer of the 42 tandem glycine riboswitch pair is typically much more highly conserved, and that which 43 aptamer is conserved depends on the regulated gene. Furthermore, our analysis also 44 reveals that singleton aptamers are more similar to either the first or second tandem 45 aptamer, again based on the regulated gene. Taken together, our findings suggest that 46 2 tandem glycine riboswitches degrade into functional singletons, with the regulated 47 gene(s) dictating which glycine-binding aptamer is conserved. 48 49 Author Summary 50The glycine riboswitch is a ncRNA responsible for the regulation of several distinct gene 51 sets in bacteria that is found with either one (singleton) or two (tandem) aptamers, each 52 of which directly senses glycine. Which aptamer is more important for gene-regulation, 53 and the functional difference between tandem and singleton aptamers, are long-54 standing questions in the riboswitch field. Like many biologically functional RNAs, 55 glycine aptamers require a specific 3D folded conformation. Thus, they have low 56 primary sequence similarity across distantly related homologs, and large changes in 57 sequence length that make creation and analysis of accurate multiple sequence 58 alignments challenging. To better understand the relationship between tandem and 59 singleton aptamers, we used a graph clustering approach that allows us to compare the 60 similarity of aptamers using metrics that measure both sequence and structure 61 similarity. Our investigation reveals that in ...