Bacteria encode diverse mechanisms for mediating interbacterial antagonism through the exchange of toxic effector proteins. Although the structure, function, and regulation of these pathways has been well established for many organisms, an understanding of their ecological and evolutionary dynamics lags behind. Type VI secretion systems (T6SS) deliver effectors between competing Gram-negative bacteria, including among mammalian gut Bacteroidales, resulting in the evolution of elaborate defense mechanisms that protect against T6SS attack. One such mechanism is the recombinase-associated acquired interbacterial defence (rAID) system, which harbors arrays of orphan immunity genes that diverge in sequence from T6SS-associated cognate immunity genes. It is not known if such sequence divergence impacts rAID orphan immunity function, or how rAID distribution across microbiomes relates to the T6SS. Here, we show that divergent rAID orphan immunity factors that possess SUKH domains allow bacteria to survive intoxication by cognate effectors. Such protection is due to high affinity protein-protein interactions between orphan immunity and effector that are comparable to that of cognate effector-immunity. Unlike other examples of T6SS effector-immunity interactions, we find that the binding interface is comprised of electrostatic interactions with a high degree of redundancy underlying its protective capacity. Finally, we quantify orphan immunity and effector gene abundance and dynamics across human gut metagenomes, revealing patterns of co-occurrence indicative of positive selection. Population genetic analyses of longitudinal data suggests that orphan immunity genes accumulate non-synonymous mutations that lie at the predicted effector-immunity interface. Together, our findings establish rAID orphan immunity genes as important bacterial fitness determinants in the human gut.

The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.

Furan is a naturally forming compound found in heat-processed foods such as coffee, canned meats, and jarred baby food. It is concurrently found with analogues including 2-methylfuran (2-MF) and 3-methylfuran (3-MF), and toxicity studies demonstrate all are potent liver toxins. Toxicity studies found 3-MF is more toxic than either furan, or 2-MF. The present analysis assesses the transcriptional response in liver samples taken from male Fischer (F344) rats exposed to furan or 3-MF from 0 to 2.0 and 0-1.0 mg/kg bw/day, respectively, for 90 days. Transcriptional analyses found decreased liver function and fatty acid metabolism are common responses to both furan and 3-MF exposure. Furan liver injury promotes a ductular reaction through Hippo and TGFB signalling, which combined with increased immune response results in ameliorating perturbed bile acid homeostasis in treated rats. Failure to activate these pathways in 3-MF exposed rats and decreased p53 activity leads to cholestasis, and increased toxicity. Finally, BMD analysis indicate many of the most sensitive pathways affected by furan and 3-MF exposure relate to metabolism - malate dehydrogenase and glucose metabolism with BMDLs of 0.03 and 0.01 mg/kg bw/day for furan and 3-MF exposure, respectively, which agrees with BMDLs previously reported for apical and microarray data.

The intensive workload associated with the preparation of high-quality DNA libraries remains a key obstacle toward widespread deployment of sequencing technologies in remote and resource-limited areas. We describe the development of single-use microfluidic devices driven by an advanced pneumatic centrifugal microfluidic platform, the PowerBlade, to automate the preparation of Illumina-compatible libraries based on adaptor ligation methodology. The developed on-chip workflow includes enzymatic DNA fragmentation coupled to end-repair, adaptor ligation, first DNA cleanup, PCR amplification, and second DNA cleanup. This complex workflow was successfully integrated into simple thermoplastic microfluidic devices that are amenable to mass production with injection molding. The system was validated by preparing, on chip, libraries from a mixture of genomic DNA extracted from three common foodborne pathogens (Listeria monocytogenes, Escherichia coli and Salmonella enterica serovar Typhimurium) and comparing them with libraries made via a manual procedure. The two types of libraries were found to exhibit similar quality control metrics (including genome coverage, assembly, and relative abundances) and led to nearly uniform coverage independent of GC content. This microfluidic technology offers a time-saving and cost-effective alternative to manual procedures and robotic-based automation, making it suitable for deployment in remote environments where technical expertise and resources might be scarce. Specifically, it facilitates field practices that involve mid- to low-throughput sequencing, such as tasks related to foodborne pathogen detection, characterization, and microbial profiling.

Humans constantly encounter new microbes, but few become long-term residents of the adult gut microbiome. Classical theories predict that colonization is determined by the availability of open niches, but it remains unclear whether other ecological barriers limit commensal colonization in natural settings. To disentangle these effects, we used a controlled perturbation with the antibiotic ciprofloxacin to investigate the dynamics of gut microbiome transmission in 22 households of healthy, cohabiting adults. Colonization was rare in three-quarters of antibiotic-taking subjects, whose resident strains rapidly recovered in the week after antibiotics ended. In contrast, the remaining antibiotic-taking subjects exhibited lasting responses, with extensive species losses and transient expansions of potential opportunistic pathogens. These subjects experienced elevated rates of commensal colonization, but only after long delays: many new colonizers underwent sudden, correlated expansions months after the antibiotic perturbation. Furthermore, strains that had previously transmitted between cohabiting partners rarely recolonized after antibiotic disruptions, showing that colonization displays substantial historical contingency. This work demonstrates that there remain substantial ecological barriers to colonization even after major microbiome disruptions, suggesting that dispersal interactions and priority effects limit the pace of community change.

Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of great importance; however, knowledge of the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics, yet the conditions under which antagonistic behaviour is favoured or disfavoured by selection in the gut are not well understood. Here, using genomics, we show that a species-specific type VI secretion system (T6SS) repeatedly acquires inactivating mutations in Bacteroides fragilis in the human gut. This result implies a fitness cost to the T6SS, but we could not identify laboratory conditions under which such a cost manifests. Strikingly, experiments in mice illustrate that the T6SS can be favoured or disfavoured in the gut depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use ecological modelling to explore the conditions that could underlie these results and find that community spatial structure modulates interaction patterns among bacteria, thereby modulating the costs and benefits of T6SS activity. Our findings point towards new integrative models for interrogating the evolutionary dynamics of type VI secretion and other modes of antagonistic interaction in microbiomes.

Determining associations between intestinal bacteria and continuously measured physiological outcomes is important for understanding the bacteria-host relationship but is not straightforward since abundance data (compositional data) are not normally distributed. To address this issue, we developed a fully Bayesian linear regression model (BRACoD; Bayesian Regression Analysis of Compositional Data) with physiological measurements (continuous data) as a function of a matrix of relative bacterial abundances. Bacteria can be classified as operational taxonomic units or by taxonomy (genus, family, etc.). Bacteria associated with the physiological measurement were identified using a Bayesian variable selection method: Stochastic Search Variable Selection. The output is a list of inclusion probabilities ([Formula: see text]) and coefficients that indicate the strength of the association ([Formula: see text]) for each bacterial taxa. Tests with simulated communities showed that adopting a cut point value of [Formula: see text] ≥ 0.3 for identifying included bacteria optimized the true positive rate (TPR) while maintaining a false positive rate (FPR) of ≤ 5%. At this point, the chances of identifying non-contributing bacteria were low and all well-established contributors were included. Comparison with other methods showed that BRACoD (at [Formula: see text] ≥ 0.3) had higher precision and a higher TPR than a commonly used center log transformed LASSO procedure (clr-LASSO) as well as higher TPR than an off-the-shelf Spike and Slab method after center log transformation (clr-SS). BRACoD was also less likely to include non-contributing bacteria that merely correlate with contributing bacteria. Analysis of a rat microbiome experiment identified 47 operational taxonomic units that contributed to fecal butyrate levels. Of these, 31 were positively and 16 negatively associated with butyrate. Consistent with their known role in butyrate metabolism, most of these fell within the Lachnospiraceae and Ruminococcaceae. We conclude that BRACoD provides a more precise and accurate method for determining bacteria associated with a continuous physiological outcome compared to clr-LASSO. It is more sensitive than a generalized clr-SS algorithm, although it has a higher FPR. Its ability to distinguish genuine contributors from correlated bacteria makes it better suited to discriminating bacteria that directly contribute to an outcome. The algorithm corrects for the distortions arising from compositional data making it appropriate for analysis of microbiome data.

Ochratoxin A (OTA) is a mycotoxin produced by species of Penicillium and Aspergillus, and is found in many commodities including cereal grains, nuts, and coffee. OTA is a renal carcinogen and nephrotoxin at high concentrations, targeting the proximal tubules. This study uses transcriptomics and the previously reported apical data (Bondy et al., 2021) to infer mode-of-action of OTA toxicity in male and female rats exposed to low doses of OTA in utero and throughout development. Our findings support a male-specific activation of the innate and adaptive immune responses in F1 pups to OTA exposure. This was not found in the female F1 pups, and may be due to female-specific increased p38 activity and VDR signaling. Differentially expressed genes related to karyomegaly, MAPK activity, and immune activation appears to develop from in utero exposure to OTA whereas those related to decreased kidney and liver function, and changes to reproductive pathways occur in both rat generations. Together, these transcriptional results confirm that dietary exposure to OTA causes renal toxicity as well as alterations to hepatic and reproductive pathways in rats. In utero exposure of rats to OTA results in sex-specific alterations in immune response pathways, VDR signaling, and p38 activity.

Given the massive and growing environmental impacts of conventional agriculture, humanity needs new methods for growing food that not only meet dietary needs but also provide for multiple ecosystem functions with potential benefits to people and biodiversity. Concepts from ecology and complex adaptive systems suggest that persistent structural heterogeneity and functional diversity are key for supporting biodiversity, ecosystem services, and resilience, but these concepts have not been extensively applied in agriculture, which is still dominated by annual monocropping systems. Perennial agriculture seems to embody these ecological concepts-particularly perennial polycultures that combine a variety of long-lived woody perennial food crops with continuous ground cover. However, our understanding of the benefits and trade-offs of such systems compared to conventional agriculture is limited, especially in temperate climates. Here, we provide a systematic and comprehensive study of the ecological attributes of 14 woody perennial polyculture farm fields to conventional annual and hay fields in the U.S. Midwest, one of the most industrialized food-producing regions in the world. We found that perennial fields had (1) more diverse soil fungal, invertebrate, plant, and bird communities but found no difference in soil bacterial communities; (2) less compacted soil; (3) denser ground cover; (4) more active carbon, organic carbon, and nitrogen and the same available phosphorus in the top layer of soil; and (5) more species of predatory, detritivorous, and herbivorous insects, and approximately fourfold higher abundance of herbivorous insects. Food production from the oldest half of perennial fields was only 14.7% of a regional corn/soy rotation by weight, but increased with the age of the perennial field and had high nutritional diversity. Together, these findings indicate that woody perennial polyculture fields in the U.S. Midwest are characterized by higher biodiversity and ecosystem functions than adjacent conventional fields. Woody perennial polycultures in the temperate north might play a role in the transition of agricultural landscapes toward sustaining both people and nature over the long term.

It has been suggested pleural effusions may develop in right heart failure in the absence of left heart disease. The incidence and prognostic significance of pleural effusions in pulmonary arterial hypertension is uncertain. Patients with pulmonary arterial hypertension followed at our tertiary care center were reviewed. Survival was examined based on the subsequent development of a pleural effusion. A total of 191 patients with pulmonary arterial hypertension met the inclusion criteria. The prevalence of pleural effusions on initial assessment was 7.3%. Among patients without a pleural effusion on initial imaging and at least one follow‐up computerized tomography (N = 142), pleural effusion developed in 27.5% (N = 39) of patients. No alternative etiology of the effusion was identified in 19 (48.7%) cases and effusions deemed related to pulmonary arterial hypertension occurred at an incident rate of 38.6 cases per 1000 person‐years. Of these, 14 (73.7%) were bilateral, 3 (15.8%) were right‐sided, and 2 (10.5%) were left‐sided. Effusion size was trace or small in 18 patients (94.7%). Development of a new pleural effusion was associated with attenuated survival in unadjusted survival analysis (HR: 3.80; 95% CI: 1.55–9.31), multivariate analysis (HR: 5.13; 95% CI: 1.86–14.16), and after the multivariate model was adjusted for concomitant pericardial effusion (HR: 4.86; 95% CI: 1.51–15.71). Negative impact on survival remained unchanged when effusions more likely related to an alternative cause were removed from analysis. In conclusion, pleural effusions can complicate pulmonary arterial hypertension in the absence of left heart disease. These effusions are frequently small in size, bilateral in location, and their presence is associated with decreased survival. Attenuated survival appears independent of the risk associated with a new pericardial effusion.

Background Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Results Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera. Conclusions Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.

The focus of this article is the application of natural language processing (NLP) for information extraction in event-based surveillance (EBS) systems. We describe common information extraction applications from open-source news articles and media sources in EBS systems, methods, value in public health, challenges and emerging developments.

ContexteLes méthodes de traitement du langage naturel (TLN) permettent aux ordinateurs d'analyser, de traiter et de tirer un sens du discours humain.Le domaine du TLN existe depuis les années 1950 (1); toutefois, les progrès de la technologie et des méthodes de ces dernières années ont rendu les applications de TLN plus faciles à mettre en oeuvre, certaines tâches menant à des meilleurs résultats que les performances humaines (2).Il existe de nombreuses applications quotidiennes du TLN, notamment la traduction automatique, la reconnaissance du pourriel et la reconnaissance vocale.Le TLN est un outil puissant dans le domaine des soins de santé en raison des volumes importants de données textuelles qui sont produites, par exemple les dossiers de santé électroniques.En effet, les dossiers de santé électroniques ont déjà fait l'objet d'applications du TLN, notamment pour la détection des proliférations mélanocytaires (3,4), du risque de démence (5) et des phénotypes neurologiques (6).Cependant, les applications du TLN dans le domaine des soins de santé vont au-delà des dossiers médicaux électroniques.Par exemple, il est possible d'identifier les personnes atteintes de la maladie d'Alzheimer à partir de leurs habitudes langagières (7).Cet article porte principalement sur l'application du TLN pour l'extraction d'informations dans les systèmes de surveillance événementielle (SSE).Nous décrivons les applications courantes de l'extraction d'informations à partir d'articles de presse et de sources médiatiques de sources ouvertes dans les SSE, les méthodes, la valeur en matière de santé publique, les difficultés et les nouveaux développements.

The human gastrointestinal tract consists of a dense and diverse microbial community, the composition of which is intimately linked to health. Extrinsic factors such as diet and host immunity are insufficient to explain the constituents of this community, and direct interactions between co-resident microorganisms have been implicated as important drivers of microbiome composition. The genomes of bacteria derived from the gut microbiome contain several pathways that mediate contact-dependent interbacterial antagonism(1-3). Many members of the Gram-negative order Bacteroidales encode the type VI secretion system (T6SS), which facilitates the delivery of toxic effector proteins into adjacent cells(4,5). Here we report the occurrence of acquired interbacterial defence (AID) gene clusters in Bacteroidales species that reside within the human gut microbiome. These clusters encode arrays of immunity genes that protect against T6SS-mediated intra- and inter-species bacterial antagonism. Moreover, the clusters reside on mobile elements, and we show that their transfer is sufficient to confer resistance to toxins in vitro and in gnotobiotic mice. Finally, we identify and validate the protective capability of a recombinase-associated AID subtype (rAID-1) that is present broadly in Bacteroidales genomes. These rAID-1 gene clusters have a structure suggestive of active gene acquisition and include predicted immunity factors of toxins derived from diverse organisms. Our data suggest that neutralization of contact-dependent interbacterial antagonism by AID systems helps to shape human gut microbiome ecology.

BACKGROUND:While the composition of the gut microbiome has now been well described by several large-scale studies, models that can account for the range of microbiome compositions that have been observed are still lacking. One model that has been well studied in macro communities and that could be useful for understanding microbiome assembly is the competitive lottery model. This model posits that groups of organisms from a regional pool of species are able to colonize the same niche and that the first species to arrive will take over the entire niche, excluding other group members.RESULTS:Here, we examined whether this model also plays a role in the assembly of the human gut microbiome, defining measures to identify groups of organisms whose distribution across samples conforms to the competitive lottery schema. Applying this model to multiple datasets with thousands of human gut microbiome samples, we identified several taxonomic groups that exhibit a lottery-like distribution, including the Akkermansia, Dialister, and Phascolarctobacterium genera. We validated that these groups exhibit lottery-like assembly in multiple independent microbiome datasets confirming that this assembly schema is universal and not cohort specific. Examining the distribution of species from these groups in the gut microbiome of developing infants, we found that the initial lottery winner can be replaced by a different member of the group. We further found that species from lottery-like groups tend to have fewer genes in their genomes, suggesting more specialized species that are less able to engage in niche differentiation.CONCLUSIONS:Combined, our findings highlight the complex and dynamic process through which microbial communities assemble and suggest that different phylogenetic groups may follow different models during this process.