Статті в журналах: "DRVE resistance-microbial"

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Povolotsky, Tatyana L., Alona Keren-Paz, and Ilana Kolodkin-Gal. "Metabolic Microenvironments Drive Microbial Differentiation and Antibiotic Resistance." Trends in Genetics 37, no. 1 (January 2021): 4–8. http://dx.doi.org/10.1016/j.tig.2020.10.007.

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O’Brien, Siobhán, Michael Baumgartner, and Alex R. Hall. "Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota." Evolution, Medicine, and Public Health 9, no. 1 (January 1, 2021): 256–66. http://dx.doi.org/10.1093/emph/eoab020.

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Abstract Background and objectives Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. Methodology Using anaerobic gut microcosms comprising E.coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. Results While cross-protection gave an advantage to antibiotic-susceptible E.coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E.coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). Conclusions and implications Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be a key for slowing the spread of resistance. Lay Summary Slowing the spread of global antibiotic resistance is an urgent task. In this paper, we ask how interactions between microbial species drive the spread of resistance. We show that antibiotic killing of susceptible microbes can free up resources for resistant microbes and allow them to thrive. Therefore, we should consider microbes in light of their social interactions to understand the spread of resistance.

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Habets, Michelle G. J. L., and Michael A. Brockhurst. "Therapeutic antimicrobial peptides may compromise natural immunity." Biology Letters 8, no. 3 (January 25, 2012): 416–18. http://dx.doi.org/10.1098/rsbl.2011.1203.

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Antimicrobial peptides (AMPs) have been proposed as a promising new class of antimicrobials despite warnings that therapeutic use could drive the evolution of pathogens resistant to our own immunity peptides. Using experimental evolution, we demonstrate that Staphylococcus aureus rapidly evolved resistance to pexiganan, a drug-candidate for diabetic leg ulcer infections. Evolved resistance was costly in terms of impaired growth rate, but costs-of-resistance were completely ameliorated by compensatory adaptation. Crucially, we show that, in some populations, experimentally evolved resistance to pexiganan provided S. aureus with cross-resistance to human-neutrophil-defensin-1, a key component of the innate immune response to infection. This unintended consequence of therapeutic use could drastically undermine our innate immune system's ability to control and clear microbial infections. Our results therefore highlight grave potential risks of AMP therapies, with implications for their development.

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Delgado-Baquerizo, Manuel, David J. Eldridge, Victoria Ochoa, Beatriz Gozalo, Brajesh K. Singh, and Fernando T. Maestre. "Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe." Ecology Letters 20, no. 10 (September 17, 2017): 1295–305. http://dx.doi.org/10.1111/ele.12826.

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Jurado, Andrea, Lucía Fernández, Ana Rodríguez, and Pilar García. "Understanding the Mechanisms That Drive Phage Resistance in Staphylococci to Prevent Phage Therapy Failure." Viruses 14, no. 5 (May 16, 2022): 1061. http://dx.doi.org/10.3390/v14051061.

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Despite occurring at the microscopic scale, the armed race between phages and their bacterial hosts involves multiple mechanisms, some of which are just starting to be understood. On the one hand, bacteria have evolved strategies that can stop the viral infection at different stages (adsorption, DNA injection and replication, biosynthesis and assembly of the viral progeny and/or release of the newly formed virions); on the other, phages have gradually evolved counterattack strategies that allow them to continue infecting their prey. This co-evolutionary process has played a major role in the development of microbial populations in both natural and man-made environments. Notably, understanding the parameters of this microscopic war will be paramount to fully benefit from the application of phage therapy against dangerous, antibiotic-resistant human pathogens. This review gathers the current knowledge regarding the mechanisms of phage resistance in the Staphylococcus genus, which includes Staphylococcus aureus, one of the most concerning microorganisms in terms of antibiotic resistance acquisition. Some of these strategies involve permanent changes to the bacterial cell via mutations, while others are transient, adaptive changes whose expression depends on certain environmental cues or the growth phase. Finally, we discuss the most plausible strategies to limit the impact of phage resistance on therapy, with a special emphasis on the importance of a rational design of phage cocktails in order to thwart therapeutic failure.

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NOWAKIEWICZ, ANETA, PRZEMYSŁAW ZIĘBA, SEBASTIAN GNAT, ALEKSANDRA TROŚCIAŃCZYK, MARCELINA OSIŃSKA, DOMINIK ŁAGOWSKI, MICHAŁ GONDEK, PRZEMYSŁAW KNYSZ, and NATALIA SZYSIAK. "Antimicrobial resistance: causes, consequences, diagnostic and therapeutic challenges in modern medicine." Medycyna Weterynaryjna 77, no. 12 (2021): 6603–2021. http://dx.doi.org/10.21521/mw.6603.

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The drug resistance of microorganisms has been a serious threat to public health for several decades. The growing problem of opportunistic infections in recent years and the wide access to antimicrobial drugs in both human and animal medicine determine and drive the complex mechanism related to the spread of antimicrobial resistance. Nevertheless, this phenomenon does not result only from certain practices related to the intensification of livestock production in recent years, which is often indicated as the main cause. Understanding the mechanisms and consequences of drug resistance requires not only the assessment of its contemporary causes, but also a retrospective look and an analysis why modern medicine, despite its extensive research capabilities and profound knowledge, continues to struggle with the problem of microbial insensitivity to most antimicrobials available today. This problem should be considered in the very broad context of the doctrine of “One Health”, which includes the dependence in the interconnected system of human–animal–environment.

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Noyes, Noelle R., Ilya B. Slizovskiy, and Randall S. Singer. "Beyond Antimicrobial Use: A Framework for Prioritizing Antimicrobial Resistance Interventions." Annual Review of Animal Biosciences 9, no. 1 (February 16, 2021): 313–32. http://dx.doi.org/10.1146/annurev-animal-072020-080638.

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Antimicrobial resistance (AMR) is a threat to animal and human health. Antimicrobial use has been identified as a major driver of AMR, and reductions in use are a focal point of interventions to reduce resistance. Accordingly, stakeholders in human health and livestock production have implemented antimicrobial stewardship programs aimed at reducing use. Thus far, these efforts have yielded variable impacts on AMR. Furthermore, scientific advances are prompting an expansion and more nuanced appreciation of the many nonantibiotic factors that drive AMR, as well as how these factors vary across systems, geographies, and contexts. Given these trends, we propose a framework to prioritize AMR interventions. We use this framework to evaluate the impact of interventions that focus on antimicrobial use. We conclude by suggesting that priorities be expanded to include greater consideration of host–microbial interactions that dictate AMR, as well as anthropogenic and environmental systems that promote dissemination of AMR.

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Herrero del Valle, Alba, and C. Axel Innis. "Prospects for antimicrobial development in the cryo-EM era – a focus on the ribosome." FEMS Microbiology Reviews 44, no. 6 (July 27, 2020): 793–803. http://dx.doi.org/10.1093/femsre/fuaa032.

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ABSTRACT Resistance to antimicrobial drugs used to treat bacterial, viral, fungal and parasitic infections is a major health concern requiring a coordinated response across the globe. An important aspect in the fight against antimicrobial resistance is the development of novel drugs that are effective against resistant pathogens. Drug development is a complex trans-disciplinary endeavor, in which structural biology plays a major role by providing detailed functional and mechanistic information on an antimicrobial target and its interactions with small molecule inhibitors. Although X-ray crystallography and nuclear magnetic resonance have until now been the methods of choice to characterize microbial targets and drive structure-based drug development, cryo-electron microscopy is rapidly gaining ground in these areas. In this perspective, we will discuss how cryo-electron microscopy is changing our understanding of an established antimicrobial target, the ribosome, and how methodological developments could help this technique become an integral part of the antimicrobial drug discovery pipeline.

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Kienesberger, Sabine, Amar Cosic, Maksym Kitsera, Sandra Raffl, Marlene Hiesinger, Eva Leitner, Bettina Halwachs, et al. "Enterotoxin tilimycin from gut-resident Klebsiella promotes mutational evolution and antibiotic resistance in mice." Nature Microbiology 7, no. 11 (October 26, 2022): 1834–48. http://dx.doi.org/10.1038/s41564-022-01260-3.

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AbstractKlebsiella spp. that secrete the DNA-alkylating enterotoxin tilimycin colonize the human intestinal tract. Numbers of toxigenic bacteria increase during antibiotic use, and the resulting accumulation of tilimycin in the intestinal lumen damages the epithelium via genetic instability and apoptosis. Here we examine the impact of this genotoxin on the gut ecosystem. 16S rRNA sequencing of faecal samples from mice colonized with Klebsiella oxytoca strains and mechanistic analyses show that tilimycin is a pro-mutagenic antibiotic affecting multiple phyla. Transient synthesis of tilimycin in the murine gut antagonized niche competitors, reduced microbial richness and altered taxonomic composition of the microbiota both during and following exposure. Moreover, tilimycin secretion increased rates of mutagenesis in co-resident opportunistic pathogens such as Klebsiella pneumoniae and Escherichia coli, as shown by de novo acquisition of antibiotic resistance. We conclude that tilimycin is a bacterial mutagen, and flares of genotoxic Klebsiella have the potential to drive the emergence of resistance, destabilize the gut microbiota and shape its evolutionary trajectory.

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Finethy, Ryan, Ine Jorgensen, Arun K. Haldar, Marcel R. de Zoete, Till Strowig, Richard A. Flavell, Masahiro Yamamoto, Uma M. Nagarajan, Edward A. Miao, and Jörn Coers. "Guanylate Binding Proteins Enable Rapid Activation of Canonical and Noncanonical Inflammasomes in Chlamydia-Infected Macrophages." Infection and Immunity 83, no. 12 (September 28, 2015): 4740–49. http://dx.doi.org/10.1128/iai.00856-15.

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Interferon (IFN)-inducible guanylate binding proteins (GBPs) mediate cell-autonomous host resistance to bacterial pathogens and promote inflammasome activation. The prevailing model postulates that these two GBP-controlled activities are directly linked through GBP-dependent vacuolar lysis. It was proposed that the rupture of pathogen-containing vacuoles (PVs) by GBPs destroyed the microbial refuge and simultaneously contaminated the host cell cytosol with microbial activators of inflammasomes. Here, we demonstrate that GBP-mediated host resistance and GBP-mediated inflammatory responses can be uncoupled. We show that PVs formed by the rodent pathogenChlamydia muridarum, so-called inclusions, remain free of GBPs and thatC. muridarumis impervious to GBP-mediated restrictions on bacterial growth. Although GBPs neither bind toC. muridaruminclusions nor restrictC. muridarumgrowth, we find that GBPs promote inflammasome activation inC. muridarum-infected macrophages. We demonstrate thatC. muridaruminfections induce GBP-dependent pyroptosis through both caspase-11-dependent noncanonical and caspase-1-dependent canonical inflammasomes. Among canonical inflammasomes, we find thatC. muridarumand the human pathogenChlamydia trachomatisactivate not only NLRP3 but also AIM2. Our data show that GBPs support fast-kinetics processing and secretion of interleukin-1β (IL-1β) and IL-18 by the NLRP3 inflammasome but are dispensable for the secretion of the same cytokines at later times postinfection. Because IFN-γ fails to induce IL-1β transcription, GBP-dependent fast-kinetics inflammasome activation can drive the preferential processing of constitutively expressed IL-18 in IFN-γ-primed macrophages in the absence of prior Toll-like receptor stimulation. Together, our results reveal that GBPs control the kinetics of inflammasome activation and thereby shape macrophage responses toChlamydiainfections.

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Moon, A., R. Veeratterapillay, M. Garthwaite, and C. Harding. "Urinary tract infection management – do the guidelines agree?" Journal of Clinical Urology 11, no. 2 (March 2018): 81–87. http://dx.doi.org/10.1177/2051415816681248.

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Urinary tract infection (UTI) is defined as the inflammatory response of the urothelium to bacterial invasion. UTI in adults is one of the most prevalent infectious diseases worldwide with a substantial financial burden on society. There is mounting concern surrounding the ongoing development of microbial resistance. In addition, the increasing resistance of organisms to broad-spectrum antibiotics is worrying. There is a continuing drive for antibiotic stewardship and more prudent prescribing of antimicrobial agents. There is currently no national UK guideline on the management of UTI in adults but the EAU, AUA and SIGN all have their separate recommendations. In this review, we discuss the existing guideline recommendations particularly relating to lower UTIs (cystitis and epididymo-orchitis), upper UTIs (pyelonephritis) and catheter-associated infections (due to their large healthcare burden). The aims are to identify common recommendations and assess how they may apply for the UK setting. This review has highlighted considerable differences in practice recommendations between the major UK, European and American guidelines. Discrepancy exists in the choice of antibiotics and for some types of infection, whether or not any guidance for treatment is offered. Antibiotic avoidance and prudent antibiotic prescribing will be key components of future strategies in reducing antimicrobial resistance.

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Woods, Laura C., Rebecca J. Gorrell, Frank Taylor, Tim Connallon, Terry Kwok, and Michael J. McDonald. "Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation." Proceedings of the National Academy of Sciences 117, no. 43 (October 14, 2020): 26868–75. http://dx.doi.org/10.1073/pnas.2005331117.

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Horizontal gene transfer (HGT) confers the rapid acquisition of novel traits and is pervasive throughout microbial evolution. Despite the central role of HGT, the evolutionary forces that drive the dynamics of HGT alleles in evolving populations are poorly understood. Here, we show that HGT alters the evolutionary dynamics of genetic variation, so that deleterious genetic variants, including antibiotic resistance genes, can establish in populations without selection. We evolve antibiotic-sensitive populations of the human pathogen Helicobacter pylori in an environment without antibiotic but with HGT from an antibiotic-resistant isolate of H. pylori. We find that HGT increases the rate of adaptation, with most horizontally transferred genetic variants establishing at a low frequency in the population. When challenged with antibiotic, this low-level variation potentiates adaptation, with HGT populations flourishing in conditions where nonpotentiated populations go extinct. By extending previous models of evolution under HGT, we evaluated the conditions for the establishment and spread of HGT-acquired alleles into recipient populations. We then used our model to estimate parameters of HGT and selection from our experimental evolution data. Together, our findings show how HGT can act as an evolutionary force that facilitates the spread of nonselected genetic variation and expands the adaptive potential of microbial populations.

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Buetti-Dinh, Antoine, Michela Ruinelli, Dorota Czerski, Cristian Scapozza, Agathe Martignier, Samuele Roman, Annapaola Caminada, and Mauro Tonolla. "Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps." PLOS ONE 16, no. 3 (March 30, 2021): e0248877. http://dx.doi.org/10.1371/journal.pone.0248877.

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The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.

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Kim, Sangman Michael, Jennifer DeFazio, Sanjiv Hyoju, Monika Krezalek, Nikolai Khodarev, Naseer Sangwan, Jack Gilbert, Olga Zaborina, Bana Jabri, and John Alverdy. "Fecal microbiota transplantation provokes systemic host immune changes that drive the clearance of lethal disseminated pathogens." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 199.19. http://dx.doi.org/10.4049/jimmunol.198.supp.199.19.

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Abstract After several iterations across medical disciplines, fecal microbiota transplantation (FMT) is now widely and effectively used to treat recurrent C. difficile infection. FMT normalizes the composition of the gut microbiota and is widely thought to mediate its protective effects by displacing pathogens in the context of the gut. We have previously shown that the microbiome of patients with severe sepsis consists of a low-diversity pathobiome dominated by multi-drug resistant pathogens. To test the hypothesis that treatment with FMT would protect against sepsis, we employed a gut-derived sepsis model that involves inoculation of a pathogen community (PC) into the gut of surgically-stressed mice. Septic mice receiving FMT derived from healthy mice via enema exhibited a dramatic increase in survival accompanied by restoration of gut microbial diversity. Intriguingly, we observed that treatment with FMT led to alterations to the host transcriptome in extra-intestinal tissues. Given the systemic effects of FMT administration, we next investigated whether FMT could influence survival in a model in which the PC was acutely disseminated via i.p. injection. Remarkably, administration of FMT in the gut markedly increased survival and drove the systemic clearance of pathogens. This suggests that the effects of FMT are not merely mediated by gut-confined colonization resistance, but also through the modulation of systemic host physiology in a way that is detrimental to pathogens. Comparative transcriptomics suggested that in both models the FMT rescue effect depends on the upregulation of the IRF3/Type I IFN signaling pathways, and using knockout mice we demonstrated that IRF3 is required for FMT-mediated protection and pathogen clearance.

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Liber, Julian A., Douglas H. Minier, Anna Stouffer-Hopkins, Judson Van Wyk, Reid Longley, and Gregory Bonito. "Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities." PeerJ 10 (January 27, 2022): e12701. http://dx.doi.org/10.7717/peerj.12701.

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Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.

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Larsen, Ida Søgaard, Andreas Mæchel Fritzen, Christian Strini Carl, Marianne Agerholm, Mads Thue Fejerskov Damgaard, Jacob Bak Holm, André Marette та ін. "Human Paneth cell α-defensin-5 treatment reverses dyslipidemia and improves glucoregulatory capacity in diet-induced obese mice". American Journal of Physiology-Endocrinology and Metabolism 317, № 1 (1 липня 2019): E42—E52. http://dx.doi.org/10.1152/ajpendo.00019.2019.

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Overnutrition is the principal cause of insulin resistance (IR) and dyslipidemia, which drive nonalcoholic fatty liver disease (NAFLD). Overnutrition is further linked to disrupted bowel function, microbiota alterations, and change of function in gut-lining cell populations, including Paneth cells of the small intestine. Paneth cells regulate microbial diversity through expression of antimicrobial peptides, particularly human α-defensin-5 (HD-5), and have shown repressed secretory capacity in human obesity. Mice were fed a 60% high-fat diet for 13 wk and subsequently treated with physiologically relevant amounts of HD-5 (0.001%) or vehicle for 10 wk. The glucoregulatory capacity was determined by glucose tolerance tests and measurements of corresponding insulin concentrations both before and during intervention. Gut microbiome composition was examined by 16S rRNA gene amplicon sequencing. HD-5-treated mice exhibited improved glucoregulatory capacity along with an ameliorated plasma and liver lipid profile. This was accompanied by specific decrease in jejunal inflammation and gut microbiota alterations including increased Bifidobacterium abundances, which correlated inversely with metabolic dysfunctions. This study provides proof of concept for the use of human defensins to improve host metabolism by mitigating the triad cluster of dyslipidemia, IR, and NAFLD.

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Labarta-Bajo, Lara, Anna Gramalla-Schmitz, Romana R. Gerner, Katelynn R. Kazane, Gregory Humphrey, Tara Schwartz, Karenina Sanders, et al. "CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection." Proceedings of the National Academy of Sciences 117, no. 40 (September 21, 2020): 24998–5007. http://dx.doi.org/10.1073/pnas.2003656117.

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Infections elicit immune adaptations to enable pathogen resistance and/or tolerance and are associated with compositional shifts of the intestinal microbiome. However, a comprehensive understanding of how infections with pathogens that exhibit distinct capability to spread and/or persist differentially change the microbiome, the underlying mechanisms, and the relative contribution of individual commensal species to immune cell adaptations is still lacking. Here, we discovered that mouse infection with a fast-spreading and persistent (but not a slow-spreading acute) isolate of lymphocytic choriomeningitis virus induced large-scale microbiome shifts characterized by increased Verrucomicrobia and reduced Firmicute/Bacteroidetes ratio. Remarkably, the most profound microbiome changes occurred transiently after infection with the fast-spreading persistent isolate, were uncoupled from sustained viral loads, and were instead largely caused by CD8 T cell responses and/or CD8 T cell-induced anorexia. Among the taxa enriched by infection with the fast-spreading virus, Akkermansia muciniphila, broadly regarded as a beneficial commensal, bloomed upon starvation and in a CD8 T cell-dependent manner. Strikingly, oral administration of A. muciniphila suppressed selected effector features of CD8 T cells in the context of both infections. Our findings define unique microbiome differences after chronic versus acute viral infections and identify CD8 T cell responses and downstream anorexia as driver mechanisms of microbial dysbiosis after infection with a fast-spreading virus. Our data also highlight potential context-dependent effects of probiotics and suggest a model in which changes in host behavior and downstream microbiome dysbiosis may constitute a previously unrecognized negative feedback loop that contributes to CD8 T cell adaptations after infections with fast-spreading and/or persistent pathogens.

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Hawkins, Shannon M., and Kenneth P. Nephew. "Unintended Consequences of Antibiotic Therapy on the Microbiome Delivers a Gut Punch in Ovarian Cancer." Cancer Research 82, no. 24 (December 16, 2022): 4511–12. http://dx.doi.org/10.1158/0008-5472.can-22-3013.

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Abstract While the early use of antibiotics during chemotherapy may be lifesaving, antibiotic therapy is associated with worse outcomes in patients with ovarian cancer during platinum chemotherapy. The study by Chambers and colleagues in this issue of Cancer Research provides mechanistic insights into how disrupting the gut microbiome with broad-spectrum antibiotics negatively influences the survival of patients with ovarian cancer and highlights the impact of the gut microbiome on tumor progression and response to therapy. Treatment of ovarian cancer models with a broad-spectrum antibiotic cocktail (ABX, vancomycin, neomycin sulfate, metronidazole, ampicillin) changed the gut microbiome and increased tumor growth and development of cisplatin resistance. Stem cells, reported to drive resistance to chemotherapy and disease recurrence in ovarian cancer, were enriched as a surprising consequence of ABX-induced microbiome disruption. Immune-competent and immune-deficient mice revealed that ABX treatment enhanced the cisplatin-induced stemness and provided evidence for immune surveillance of ovarian cancer stem cells through the gut microbiome. Two gut-derived metabolites, indole-3-propionic acid and indoxyl sulfate, suppressed by ABX treatment and reestablished with cecal microbial transplantation colonization of ABX-treated mice, were identified as potential effectors connecting the gut microbiome to ovarian cancer growth. This clinically relevant study opens new therapeutic opportunities for patients—one aimed at interventions to increase platinum sensitivity and another aimed at preventing the potential adverse effects of broad-spectrum antibiotic treatment. Both represent paradigm changes to standard care. See related article by Chambers et al., p. 4654

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Tariq, Akash, Jordi Sardans, Josep Peñuelas, Zhihao Zhang, Corina Graciano, Fanjiang Zeng, Olusanya Abiodun Olatunji, Abd Ullah, and Kaiwen Pan. "Intercropping of Leguminous and Non-Leguminous Desert Plant Species Does Not Facilitate Phosphorus Mineralization and Plant Nutrition." Cells 11, no. 6 (March 15, 2022): 998. http://dx.doi.org/10.3390/cells11060998.

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More efficient use of soil resources, such as nitrogen (N) and phosphorus (P), can improve plant community resistance and resilience against drought in arid and semi-arid lands. Intercropping of legume and non-legumes can be an effective practice for enhancing P mineralization uptake, and plant nutrient status. However, it remains unclear how intercropping systems using desert plant species impact soil-plant P fractions and how they affect N and water uptake capacity. Alhagi sparsifolia (a legume) and Karelinia caspia (a non-legume) are dominant plant species in the Taklamakan Desert in Xinjiang Province, China. However, there is a lack of knowledge of whether these species, when intercropped, can trigger synergistic processes and mechanisms that drive more efficient use of soil resources. Thus, in a field experiment over two years, we investigated the impact of monoculture and intercropping of these plant species on soil-plant P fractions and soil-plant nutrients. Both plant species’ foliar nutrient (N, P, and K) concentrations were higher under monoculture than intercropping (except K in K. caspia). Nucleic acid P was higher in the monoculture plots of A. sparsifolia, consistent with higher soil labile P, while metabolic P was higher in monoculture K. caspia, associated with higher soil moderately labile Pi. However, both species had a higher residual P percentage in the intercropping system. Soils from monoculture and intercropped plots contained similar microbial biomass carbon (MBC), but lower microbial biomass N:microbial biomass phosphorus (MBN:MBP) ratio associated with reduced N-acetylglucosaminidase (NAG) activity in the intercropped soils. This, together with the high MBC:MBN ratio in intercropping and the lack of apparent general effects of intercropping on MBC:MBP, strongly suggest that intercropping improved microbe N- but not P-use efficiency. Interestingly, while EC and SWC were higher in the soil of the K. caspia monoculture plots, EC was significantly lower in the intercropped plots. Plants obtained better foliar nutrition and soil P mineralization in monocultures than in intercropping systems. The possible positive implications of intercropping for reducing soil salinization and improving soil water uptake and microbial N-use efficiency could have advantages in the long term and its utilization should be explored further in future studies.

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Deshpande, Devyani, Shashikant Srivastava, Sandirai Musuka, and Tawanda Gumbo. "Thioridazine as Chemotherapy for Mycobacterium avium Complex Diseases." Antimicrobial Agents and Chemotherapy 60, no. 8 (May 23, 2016): 4652–58. http://dx.doi.org/10.1128/aac.02985-15.

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ABSTRACTMycobacterium avium-intracellularecomplex (MAC) causes an intractable intracellular infection that presents as chronic pulmonary disease. Currently, therapy consists of ethambutol and macrolides and takes several years to complete. The neuroleptic phenothiazine thioridazine kills mycobacteria by inhibiting the electron transport chain. In several experiments with bacterial populations of up to 1012CFU/ml, we failed to isolate any bacteria resistant to 3 times the MIC of thioridazine, suggesting the absence of resistant mutants at bacterial burdens severalfold higher than those encountered in patients. In the hollow-fiber model of intracellular MAC (HFS-MAC), thioridazine achieved an extracellular half-life of 16.8 h and an intracellular half-life of 19.7 h. Thioridazine concentrations were >28,000-fold higher inside infected macrophages than in the HFS-MAC central compartment (equivalent to plasma). Thioridazine maximal kill was 5.20 ± 0.75 log10CFU/ml on day 7 (r2= 0.96) and 7.19 ± 0.31 log10CFU/ml on day 14 (r2= 0.99), the highest seen with any drug in the system. Dose fractionation studies revealed that thioridazine efficacy and acquired drug resistance were driven by the peak concentation-to-MIC ratio, with a 50% effective concentration (EC50) of 2.78 ± 0.44 for microbial killing. Acquired drug resistance was encountered by day 21 with suboptimal doses, demonstrating that fluctuating drug concentrations drive evolution faster than static concentrations in mutation frequency studies. However, the thioridazine EC50changed 16.14-fold when the concentration of fetal bovine serum was changed from 0% to 50%, suggesting that intracellular potency could be heavily curtailed by protein binding. Efficacy in patients will depend on the balance between trapping of the drug in the pulmonary system and the massive intracellular concentrations versus very high protein binding of thioridazine.

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Isabella, Odis Adaora. "Conceptual Framework for Epidemics and Vaccination Dilemma." TEXILA INTERNATIONAL JOURNAL OF PUBLIC HEALTH 10, no. 1 (March 30, 2022): 66–79. http://dx.doi.org/10.21522/tijph.2013.10.01.art006.

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Outbreaks of diseases have positive and negative effects on humans. An example of the positive epidemic dilemma was seen in the 2020 lockdown across the world where families spent quality time together and couples seeking for the fruit of the womb conceived after many years, working from home was introduced, Lagosians working from home reduced stress from traffic, remote jobs were increased, online zoom, Webex webinars, online surveys, seminars, conference, Viva Voca, graduation and growth for online business and banking. Apps were available for the masses to access health online, known as Telemedicine. While the negative epidemics dilemma includes loss of jobs, slow down in economy across the world, poverty, drug abuse, self–medication, Anti-microbial resistance, child abuse, rape, divorce, shadow pandemic, death, and no access to education for those that do not have internet facilities to learn/study/school online. Vaccine’s hesitancy is an established dilemma that contributes to significant health challenges which cause a high rate of infant sickness and death. There are certain factors like cultural, social, demographic, and psychosocial factors that contribute to the vaccine dilemma. This conceptual framework illustrates the factors that drive epidemics and vaccine dilemma, which can be vaccination acceptance and hesitancy. For an intervention to be implemented successfully, we need to understand the triggers of epidemics and vaccination dilemma. The socio-demographic characteristics like age, sex, marital status, level of education, choice of hospital, employment status, level of income, health insurance status and the number of children is significantly associated with vaccine uptake among parents.

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Sullivan, Matthew J., Kelvin G. K. Goh, and Glen C. Ulett. "Regulatory cross-talk supports resistance to Zn intoxication in Streptococcus." PLOS Pathogens 18, no. 7 (July 21, 2022): e1010607. http://dx.doi.org/10.1371/journal.ppat.1010607.

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Metals such as copper (Cu) and zinc (Zn) are important trace elements that can affect bacterial cell physiology but can also intoxicate bacteria at high concentrations. Discrete genetic systems for management of Cu and Zn efflux have been described in several bacteria pathogens, including streptococci. However, insight into molecular cross-talk between systems for Cu and Zn management in bacteria that drive metal detoxification, is limited. Here, we describe a biologically consequential cross-system effect of metal management in group B Streptococcus (GBS) governed by the Cu-responsive copY regulator in response to Zn. RNAseq analysis of wild-type (WT) and copY-deficient GBS subjected to metal stress revealed unique transcriptional links between the systems for Cu and Zn detoxification. We show that the Cu-sensing role of CopY extends beyond Cu and enables CopY to regulate Cu and Zn stress responses that effect changes in gene function for central cellular processes, including riboflavin synthesis. CopY also supported GBS intracellular survival in human macrophages and virulence during disseminated infection in mice. In addition, we show a novel role for CovR in modulating GBS resistance to Zn intoxication. Identification of the Zn resistome of GBS using TraDIS revealed a suite of genes essential for GBS growth in metal stress. Several of the genes identified are novel to systems that support bacterial survival in metal stress and represent a diverse set of mechanisms that underpin microbial metal homeostasis during cell stress. Overall, this study reveals a new and important mechanism of cross-system complexity driven by CopY in bacteria to regulate cellular management of metal stress and survival.

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Laurin, E., M. Stormoen, C. Revie, and J. Sanchez. "A stepwise integrated risk-assessment framework in aquaculture: the case of sea lice tolerance to freshwater treatments on salmon farms." Aquaculture Environment Interactions 12 (October 22, 2020): 417–28. http://dx.doi.org/10.3354/aei00373.

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Aquaculture studies are often faced with data limitations when carrying out a quantitative risk assessment. Consolidating results from a literature search of potentially applicable methods, we propose a stepwise integrated methods approach that incorporates foundations from an antimicrobial resistance framework, the Office International Epizooties risk model, quantitative microbial risk assessment and infectious disease transmission models. We suggest that an initial ranking profile can be used to prioritize more in-depth qualitative and quantitative risk assessments, when data are available. The ranking method was done using a software that provides practical and interactive graphics for visualizing the impact of different factors and their respective weights on the likelihood of undesirable events (hazards) occurring. For this step, we illustrate how to include available data to obtain ranking results for decision makers using information from a recent sea lice freshwater tolerance literature review (Groner et al. 2019) that identified a gap in quantitative data. In our case example, for copepodid sea lice life stages, hypothetically changing how much experts believe that location and time are important factors revealed the most impact on the ranking for different degrees of freshwater tolerance evolution (no evolution, various partial options, known evolution). The factors ‘location’ and ‘time’, as well as ‘freshwater treatment’, have the greatest impact on the ranking for the preadult sea lice life-stages model. Results from our proposed ranking method can help to drive decisions around interpreting the various factors as they apply to mitigation planning and prioritizing those that should be included in further research. Additionally, we identify where quantitative data could be incorporated, as they become available, into a full risk assessment model with suggested models for a freshwater tolerance risk analysis framework.

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Dafflon, Baptiste, Susan Hubbard, Craig Ulrich, John Peterson, Yuxin Wu, Haruko Wainwright, and Timothy J. Kneafsey. "Geophysical estimation of shallow permafrost distribution and properties in an ice-wedge polygon-dominated Arctic tundra region." GEOPHYSICS 81, no. 1 (January 1, 2016): WA247—WA263. http://dx.doi.org/10.1190/geo2015-0175.1.

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Shallow permafrost distribution and characteristics are important for predicting ecosystem feedbacks to a changing climate over decadal to century timescales because they can drive active layer deepening and land surface deformation, which in turn can significantly affect hydrologic and biogeochemical responses, including greenhouse gas dynamics. As part of the U.S. Department of Energy Next-Generation Ecosystem Experiments-Arctic, we have investigated shallow Arctic permafrost characteristics at a site in Barrow, Alaska, with the objective of improving our understanding of the spatial distribution of shallow permafrost, its associated properties, and its links with landscape microtopography. To meet this objective, we have acquired and integrated a variety of information, including electric resistance tomography data, frequency-domain electromagnetic induction data, laboratory core analysis, petrophysical studies, high-resolution digital surface models, and color mosaics inferred from kite-based landscape imaging. The results of our study provide a comprehensive and high-resolution examination of the distribution and nature of shallow permafrost in the Arctic tundra, including the estimation of ice content, porosity, and salinity. Among other results, porosity in the top 2 m varied between 85% (besides ice wedges) and 40%, and was negatively correlated with fluid salinity. Salinity directly influenced ice and unfrozen water content and indirectly influenced the soil organic matter content. A relatively continuous but depth-variable increase in salinity led to a partially unfrozen saline layer (cryopeg) located below the top of the permafrost. The cryopeg environment could lead to year-round microbial production of greenhouse gases. Results also indicated a covariability between topography and permafrost characteristics including ice-wedge and salinity distribution. In addition to providing insight about the Arctic ecosystem, through integration of lab-based petrophysical results with field data, this study also quantified the key controls on electric resistivity at this Arctic permafrost site, including salinity, porosity, water content, ice content, soil organic matter content, and lithologic properties.

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Thiele Orberg, Erik, Sascha Göttert, Andreas Hiergeist, Elisabeth Meedt, Karin Kleigrewe, Wolfgang Herr, Florian Bassermann, et al. "Microbial-Derived Metabolites Induce Epithelial Recovery Via the Sting Pathway in Mice and Men and Protect from Graft-Versus-Host Disease." Blood 138, Supplement 1 (November 5, 2021): 87. http://dx.doi.org/10.1182/blood-2021-147794.

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Abstract Background: Graft-versus-host disease (GVHD) is a dreaded complication after allogeneic stem-cell transplantation (ASCT). Previously, we and others showed that activation of type I interferon (IFN-I) inducing pathways such as RIG-I/MAVS or cGAS-STING can promote the integrity of the intestinal barrier and limit GVHD (Fischer et al., Sci Transl Med, 2017). However, the signals that drive these protective IFN-I responses are poorly understood. Commensal microbiota can (i) have distant effects on immune responses through modulation of IFN-I signaling (Steed et al, Science, 2017; Swimm et al, Blood, 2018) and (ii) predict mortality in ASCT patients (Peled et al., N Engl J Med, 2020). We hypothesized that microbiota-derived products such as microbial metabolites engage IFN-I signaling in immune and non-immune cells poising them for induction of protective responses. We established a prospective, multi-centric clinical study in patients newly diagnosed with acute leukemia and performed longitudinal stool sampling to track changes in microbial community composition and metabolites expression levels. Submitted as a separate abstract to ASH 2021 (Orberg & Meedt et al.), we show that patients with high metabolite expression going into ASCT are less likely to develop GVHD. In this study, we translate our clinical observations to mouse models of acute GVHD and human and mouse intestinal organoids to uncover the molecular mechanisms via which metabolites protect the intestinal barrier during ASCT. Methods: Stool samples from ASCT patients were obtained in Munich and at Regensburg in accordance to IRB-approved study protocols. Patients were sampled at initial diagnosis (Dx), prior to conditioning and weekly after ASCT up to day 28. We analyzed samples by 16S rRNA sequencing and mass spectrometry to obtain a complete picture of microbiome composition and function. Next, we tested metabolites which we detected in patients (desaminotyrosine [DAT], indole-3-carboxaldehyde [ICA]) as treatment in preclinical models in ASCT and GVHD mouse models. Outcomes were assessed by a novel organoid recovery assay in addition to established read-outs. To obtain a mechanistic understanding of the signaling pathways involved, we stimulated WT or IFN-I-signaling-impaired mouse (incl. STING -/-, MAVS -/-, IFNαR -/-) as well as human intestinal crypt-derived organoids with metabolites. Results: Here, we present a 64-year-old female patient diagnosed with AML who received a 9/10 HLA-matched ASCT. At day 7, i.v. antibiotics were started due to fever and Enterococcus bacteraemia. At day 15, the patient developed skin and GI GVHD (Glucksberg III). At the timepoint initial diagnosis (Dx), i.e. the timepoint when we diagnosed AML but before therapy was initiated, we detected rich alpha diversity (Panel 1a) in the patient's stool. Flavonifractor plautii, a producer of the metabolite DAT, was detectable (Panel 1b). We observed high-level expression of metabolites including short-chain fatty acids, DAT, ICA and secondary bile acids (Panel 1c). Following ASCT, and especially at the early time-points day 0 and day 7, alpha diversity and metabolite expression declined drastically. We confirmed this trend in our multi-centric cohort of ASCT patients by comparing levels of DAT and ICA sampled at admission to the transplantation ward (Conditioning) versus at clinical diagnosis of GVHD: in patients with GVHD, metabolite levels were drastically reduced (Panel 2). Next, we prophylactically administered metabolites in a major mismatch mouse ASCT model. Metabolite-treated mice showed significantly showed better outcomes in our organoid recovery assay, which measures the ability of intestinal stem cells to recover after allogeneic injury (Panel 3). This effect that was abrogated in STING -/- recipients. Metabolite stimulation of mouse small intestinal organoids promoted organoid numbers and size, and required intact STING signaling (Panel 4a). Human colon organoids also responded to DAT and ICA, however the metabolite effect was lost when co-administered with the STING-inhibitor H151. Conclusions: We identify that microbial-derived metabolites detected in patients can engage the STING pathway in humans and mice to confer resistance from immune damage. Thus, prophylactic administration of metabolite cocktails or bacterial consortia that can produce these metabolites may reduce occurrence of GVHD in ASCT patients. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

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Baumgartner, Michael, Katia R. Pfrunder-Cardozo, and Alex R. Hall. "Microbial community composition interacts with local abiotic conditions to drive colonization resistance in human gut microbiome samples." Proceedings of the Royal Society B: Biological Sciences 288, no. 1947 (March 24, 2021). http://dx.doi.org/10.1098/rspb.2020.3106.

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Biological invasions can alter ecosystem stability and function, and predicting what happens when a new species or strain arrives remains a major challenge in ecology. In the mammalian gastrointestinal tract, susceptibility of the resident microbial community to invasion by pathogens has important implications for host health. However, at the community level, it is unclear whether susceptibility to invasion depends mostly on resident community composition (which microbes are present), or also on local abiotic conditions (such as nutrient status). Here, we used a gut microcosm system to disentangle some of the drivers of susceptibility to invasion in microbial communities sampled from humans. We found resident microbial communities inhibited an invading Escherichia coli strain, compared to community-free control treatments, sometimes excluding the invader completely (colonization resistance). These effects were stronger at later time points, when we also detected altered community composition and nutrient availability. By separating these two components (microbial community and abiotic environment), we found taxonomic composition played a crucial role in suppressing invasion, but this depended critically on local abiotic conditions (adapted communities were more suppressive in nutrient-depleted conditions). This helps predict when resident communities will be most susceptible to invasion, with implications for optimizing treatments based on microbiota management.

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Plata, Germán, Nielson T. Baxter, Dwi Susanti, Alyssa Volland-Munson, Dharanesh Gangaiah, Akshitha Nagireddy, Shrinivasrao P. Mane, Jayanth Balakuntla, Troy B. Hawkins, and Arvind Kumar Mahajan. "Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome." Communications Biology 5, no. 1 (April 1, 2022). http://dx.doi.org/10.1038/s42003-022-03239-6.

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AbstractAntimicrobial growth promoters (AGP) have played a decisive role in animal agriculture for over half a century. Despite mounting concerns about antimicrobial resistance and demand for antibiotic alternatives, a thorough understanding of how these compounds drive performance is missing. Here we investigate the functional footprint of microbial communities in the cecum of chickens fed four distinct AGP. We find relatively few taxa, metabolic or antimicrobial resistance genes similarly altered across treatments, with those changes often driven by the abundances of core microbiome members. Constraints-based modeling of 25 core bacterial genera associated increased performance with fewer metabolite demands for microbial growth, pointing to altered nitrogen utilization as a potential mechanism of narasin, the AGP with the largest performance increase in our study. Untargeted metabolomics of narasin treated birds aligned with model predictions, suggesting that the core cecum microbiome might be targeted for enhanced performance via its contribution to host-microbiota metabolic crosstalk.

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da Silva, Giarlã Cunha, Osiel Silva Gonçalves, Jéssica Nogueira Rosa, Kiara Campos França, Janine Thérèse Bossé, Mateus Ferreira Santana, Paul Richard Langford, and Denise Mara Soares Bazzolli. "Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species." Frontiers in Microbiology 12 (January 6, 2022). http://dx.doi.org/10.3389/fmicb.2021.773284.

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Mobile genetic elements (MGEs) and antimicrobial resistance (AMR) drive important ecological relationships in microbial communities and pathogen-host interaction. In this study, we investigated the resistome-associated mobilome in 345 publicly available Pasteurellaceae genomes, a large family of Gram-negative bacteria including major human and animal pathogens. We generated a comprehensive dataset of the mobilome integrated into genomes, including 10,820 insertion sequences, 2,939 prophages, and 43 integrative and conjugative elements. Also, we assessed plasmid sequences of Pasteurellaceae. Our findings greatly expand the diversity of MGEs for the family, including a description of novel elements. We discovered that MGEs are comparable and dispersed across species and that they also co-occur in genomes, contributing to the family’s ecology via gene transfer. In addition, we investigated the impact of these elements in the dissemination and shaping of AMR genes. A total of 55 different AMR genes were mapped to 721 locations in the dataset. MGEs are linked with 77.6% of AMR genes discovered, indicating their important involvement in the acquisition and transmission of such genes. This study provides an uncharted view of the Pasteurellaceae by demonstrating the global distribution of resistance genes linked with MGEs.

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Hemme, Christopher L., Stefan J. Green, Lavanya Rishishwar, Om Prakash, Angelica Pettenato, Romy Chakraborty, Adam M. Deutschbauer, et al. "Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community." mBio 7, no. 2 (April 5, 2016). http://dx.doi.org/10.1128/mbio.02234-15.

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ABSTRACT Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe 2+ /Pb 2+ permeases, most denitrification enzymes, and cytochrome c 553 , were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co 2+ /Zn 2+ /Cd 2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. IMPORTANCE Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

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Prokchorchik, Maxim, Ankita Pandey, Hayoung Moon, Wanhui Kim, Hyelim Jeon, Gayoung Jung, Jay Jayaraman, et al. "Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea." Microbial Genomics 6, no. 11 (November 1, 2020). http://dx.doi.org/10.1099/mgen.0.000461.

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Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) threatens the cultivation of important crops worldwide. We sequenced 30 RSSC phylotype I ( R. pseudosolanacearum ) strains isolated from pepper (Capsicum annuum) and tomato (Solanum lycopersicum) across the Republic of Korea. These isolates span the diversity of phylotype I, have extensive effector repertoires and are subject to frequent recombination. Recombination hotspots among South Korean phylotype I isolates include multiple predicted contact-dependent inhibition loci, suggesting that microbial competition plays a significant role in Ralstonia evolution. Rapid diversification of secreted effectors presents challenges for the development of disease-resistant plant varieties. We identified potential targets for disease resistance breeding by testing for allele-specific host recognition of T3Es present among South Korean phyloype I isolates. The integration of pathogen population genomics and molecular plant pathology contributes to the development of location-specific disease control and development of plant cultivars with durable resistance to relevant threats.

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Ma, Ning, Yiwei Sun, Jiashun Chen, Zengkai Qi, Chunchen Liu, and Xi Ma. "Micro-Coevolution of Genetics Rather Than Diet With Enterotype in Pigs." Frontiers in Nutrition 9 (March 22, 2022). http://dx.doi.org/10.3389/fnut.2022.846974.

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Based on the characteristic of low diarrhea in native Chinese breeds, we introduce the enterotype model for piglets, which is a new perspective to decipher the colonization and the transition of the gut microbiota among various pig breeds. After eliminating environmental influences represented by diet, the microbiota, mainly shaped by host genetics, is focused. Three representative enterotype clusters were identified, which were represented by Bacteroides, Streptococcus, and Lactobacillus. Chinese native breeds were distributed in enterotype 1 (E1) and E3, which collectively drove the diversification and functionality of the microbial community of various Chinese pig breeds. Next, the Lactobacillus reuteri (L. reuteri), which is the representative strain of E3, was specifically isolated in all three enterotypes. The excellent stress-resistance of L. reuteri-E3 not only highlighted the stronger disease resistance of Chinese breeds but also had a great potential to intervene in weaned piglet diseases. Enterotype classification based on host genetics is much more deterministic and predictable, clarifying the driver of the host-microbiome dynamics and constructing the picture of the micro-coevolution of human host genetics with the gut microbiome.

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Cezar, Renaud, Audrey Winter, Delphine Desigaud, Manuela Pastore, Lucy Kundura, Anne-Marie Dupuy, Chantal Cognot, et al. "Identification of distinct immune activation profiles in adult humans." Scientific Reports 10, no. 1 (November 30, 2020). http://dx.doi.org/10.1038/s41598-020-77707-6.

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AbstractLatent infectious agents, microbial translocation, some metabolites and immune cell subpopulations, as well as senescence modulate the level and quality of activation of our immune system. Here, we tested whether various in vivo immune activation profiles may be distinguished in a general population. We measured 43 markers of immune activation by 8-color flow cytometry and ELISA in 150 adults, and performed a double hierarchical clustering of biomarkers and volunteers. We identified five different immune activation profiles. Profile 1 had a high proportion of naïve T cells. By contrast, Profiles 2 and 3 had an elevated percentage of terminally differentiated and of senescent CD4+ T cells and CD8+ T cells, respectively. The fourth profile was characterized by NK cell activation, and the last profile, Profile 5, by a high proportion of monocytes. In search for etiologic factors that could determine these profiles, we observed a high frequency of naïve Treg cells in Profile 1, contrasting with a tendency to a low percentage of Treg cells in Profiles 2 and 3. Moreover, Profile 5 tended to have a high level of 16s ribosomal DNA, a direct marker of microbial translocation. These data are compatible with a model in which specific causes, as the frequency of Treg or the level of microbial translocation, shape specific profiles of immune activation. It will be of interest to analyze whether some of these profiles drive preferentially some morbidities known to be fueled by immune activation, as insulin resistance, atherothrombosis or liver steatosis.

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Chopyk, Jessica, Daniel J. Nasko, Sarah Allard, Anthony Bui, Mihai Pop, Emmanuel F. Mongodin, and Amy R. Sapkota. "Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond." Environmental Microbiome 15, no. 1 (October 28, 2020). http://dx.doi.org/10.1186/s40793-020-00365-8.

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Abstract Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

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Leech, John, Raul Cabrera-Rubio, Aaron M. Walsh, Guerrino Macori, Calum J. Walsh, Wiley Barton, Laura Finnegan, et al. "Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants." mSystems 5, no. 6 (November 10, 2020). http://dx.doi.org/10.1128/msystems.00522-20.

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ABSTRACT Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of “industrialization” of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential. IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.

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Cheaib, Bachar, Hamza Seghouani, Martin Llewellyn, Katherine Vandal-Lenghan, Pierre-Luc Mercier, and Nicolas Derome. "The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance." Animal Microbiome 3, no. 1 (January 5, 2021). http://dx.doi.org/10.1186/s42523-020-00063-3.

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Abstract Background Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial habitats, free-living (water), and host-associated (skin and gut) were experimentally exposed to either a constant or gradual selection regime exerted by two sublethal cadmium chloride dosages (CdCl2). Yellow Perch (Perca flavescens) was used as a piscivorous ecotoxicological model. Using 16S rDNA gene based metataxonomics, quantitative diversity metrics of water, skin and gut microbial communities were characterized along with development and across experimental conditions. Results After 30 days, constant and gradual selection regimes drove a significant alpha diversity increase for both skin and gut microbiota. In the skin, pervasive negative correlations between taxa in both selection regimes in addition to the taxonomic convergence with the environmental bacterial community, suggest a loss of colonisation resistance resulting in the dysbiosis of yellow perch microbiota. Furthermore, the network connectivity in gut microbiome was exclusively maintained by rare (low abundance) OTUs, while most abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to fish pathogens such as Flavobacterium. Finally, the mathematical modelling of community assembly using both non-linear least squares models (NLS) based estimates of migration rates and normalized stochasticity ratios (NST) based beta-diversity distances suggested neutral processes drove by taxonomic drift in host and water communities for almost all treatments. The NLS models predicted higher demographic stochasticity in the cadmium-free host and water microbiomes, however, NST models suggested higher ecological stochasticity under perturbations. Conclusions Neutral models agree that water and host-microbiota assembly promoted by rare taxa have evolved predominantly under neutral processes with potential involvement of deterministic forces sourced from host filtering and cadmium selection. The early signals of perturbations in the skin microbiome revealed antagonistic interactions by a preponderance of negative correlations in the co-abundance networks. Our findings enhance our understanding of community assembly host-associated and free-living under anthropogenic selective pressure.

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Seed, Kimberley D., Minmin Yen, B. Jesse Shapiro, Isabelle J. Hilaire, Richelle C. Charles, Jessica E. Teng, Louise C. Ivers, Jacques Boncy, Jason B. Harris, and Andrew Camilli. "Evolutionary consequences of intra-patient phage predation on microbial populations." eLife 3 (August 26, 2014). http://dx.doi.org/10.7554/elife.03497.

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The impact of phage predation on bacterial pathogens in the context of human disease is not currently appreciated. Here, we show that predatory interactions of a phage with an important environmentally transmitted pathogen, Vibrio cholerae, can modulate the evolutionary trajectory of this pathogen during the natural course of infection within individual patients. We analyzed geographically and temporally disparate cholera patient stool samples from Haiti and Bangladesh and found that phage predation can drive the genomic diversity of intra-patient V. cholerae populations. Intra-patient phage-sensitive and phage-resistant isolates were isogenic except for mutations conferring phage resistance, and moreover, phage-resistant V. cholerae populations were composed of a heterogeneous mix of many unique mutants. We also observed that phage predation can significantly alter the virulence potential of V. cholerae shed from cholera patients. We provide the first molecular evidence for predatory phage shaping microbial community structure during the natural course of infection in humans.

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Keen, Eric C., Valery V. Bliskovsky, Francisco Malagon, James D. Baker, Jeffrey S. Prince, James S. Klaus, and Sankar L. Adhya. "Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation." mBio 8, no. 1 (January 17, 2017). http://dx.doi.org/10.1128/mbio.02115-16.

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ABSTRACT Bacteriophages infect an estimated 10 23 to 10 25 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub “superspreaders,” releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications. IMPORTANCE Bacteriophages (phages), viruses that infect bacteria, are the planet’s most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed “superspreaders,” that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.

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Bolaji, Ayooluwa J., Joey C. Wan, Christopher L. Manchur, Yvonne Lawley, Teresa R. de Kievit, W. G. Dilantha Fernando, and Mark F. Belmonte. "Microbial Community Dynamics of Soybean (Glycine max) Is Affected by Cropping Sequence." Frontiers in Microbiology 12 (February 11, 2021). http://dx.doi.org/10.3389/fmicb.2021.632280.

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The microbial composition of the rhizosphere soil could be an important determinant of crop yield, pathogen resistance, and other beneficial attributes in plants. However, little is known about the impact of cropping sequences on microbial community dynamics, especially in economically important species like soybean. Using 2-year crop sequences of corn-soybean, canola-soybean, and soybean-soybean, we investigated how crops from the previous growing season influenced the structure of the microbiome in both the bulk soil and soybean rhizosphere. A combination of marker-based Illumina sequencing and bioinformatics analyses was used to show that bacterial species richness and evenness in the soybean rhizosphere soil were similar following canola and soybean compared to a previous corn sequence. However, fungal species richness and evenness remained unaffected by crop sequence. In addition, bacterial and fungal species diversity in both the bulk and soybean rhizosphere soil were not influenced by crop sequence. Lastly, the corn-soybean sequence significantly differed in the relative abundance of certain bacterial and fungal classes in both the soybean rhizosphere and bulk soil. While canola-soybean and a continuous soybean sequence did not, suggesting that a preceding corn sequence may reduce the occurrence of overall bacterial and fungal community members. For the present study, crop sequence impacts bacterial diversity and richness in both the bulk soil and soybean rhizosphere soil whereas fungal diversity and richness are resilient to crop sequence practices. Together, these findings could help drive decision making for annual crop and soil management practices.

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Li, Liangzhi, Zhenghua Liu, Delong Meng, Xueduan Liu, Xing Li, Ming Zhang, Jiemeng Tao, Yabing Gu, Shuiping Zhong, and Huaqun Yin. "Comparative Genomic Analysis Reveals the Distribution, Organization, and Evolution of Metal Resistance Genes in the GenusAcidithiobacillus." Applied and Environmental Microbiology 85, no. 2 (November 2, 2018). http://dx.doi.org/10.1128/aem.02153-18.

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ABSTRACTMembers of the genusAcidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genusAcidithiobacillusto answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes inAcidithiobacillusspp. The results showed that the evolutionary history of metal resistance genes inAcidithiobacillusspp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes inAcidithiobacillusspp. were acquired by early HGT events from species that shared habitats withAcidithiobacillusspp., such asAcidihalobacter,Thiobacillus,Acidiferrobacter, andThiomonasspecies. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizingAcidithiobacillus ferridurans,Acidithiobacillus ferrivorans, andAcidithiobacillus ferrooxidansand were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability ofAcidithiobacillusspp. to adapt to harsh environments. Altogether, the results suggested thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes inAcidithiobacillusspp.IMPORTANCEHorizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT inAcidithiobacillusspecies in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved inAcidithiobacillusare still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting thatAcidithiobacillusspp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies ofAcidithiobacillusspp.

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Bates, Kieran A., Ulf Sommer, Kevin P. Hopkins, Jennifer M. G. Shelton, Claudia Wierzbicki, Christopher Sergeant, Benjamin Tapley, et al. "Microbiome function predicts amphibian chytridiomycosis disease dynamics." Microbiome 10, no. 1 (March 10, 2022). http://dx.doi.org/10.1186/s40168-021-01215-6.

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Abstract Background The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood. Methods Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection. Results Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes. Conclusions Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection.

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Pinto, Yishay, Sigal Frishman, Sondra Turjeman, Adi Eshel, Meital Nuriel-Ohayon, Oshrit Shrossel, Oren Ziv, et al. "Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis." Gut, January 10, 2023, gutjnl—2022–328406. http://dx.doi.org/10.1136/gutjnl-2022-328406.

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ObjectiveGestational diabetes mellitus (GDM) is a condition in which women without diabetes are diagnosed with glucose intolerance during pregnancy, typically in the second or third trimester. Early diagnosis, along with a better understanding of its pathophysiology during the first trimester of pregnancy, may be effective in reducing incidence and associated short-term and long-term morbidities.DesignWe comprehensively profiled the gut microbiome, metabolome, inflammatory cytokines, nutrition and clinical records of 394 women during the first trimester of pregnancy, before GDM diagnosis. We then built a model that can predict GDM onset weeks before it is typically diagnosed. Further, we demonstrated the role of the microbiome in disease using faecal microbiota transplant (FMT) of first trimester samples from pregnant women across three unique cohorts.ResultsWe found elevated levels of proinflammatory cytokines in women who later developed GDM, decreased faecal short-chain fatty acids and altered microbiome. We next confirmed that differences in GDM-associated microbial composition during the first trimester drove inflammation and insulin resistance more than 10 weeks prior to GDM diagnosis using FMT experiments. Following these observations, we used a machine learning approach to predict GDM based on first trimester clinical, microbial and inflammatory markers with high accuracy.ConclusionGDM onset can be identified in the first trimester of pregnancy, earlier than currently accepted. Furthermore, the gut microbiome appears to play a role in inflammation-induced GDM pathogenesis, with interleukin-6 as a potential contributor to pathogenesis. Potential GDM markers, including microbiota, can serve as targets for early diagnostics and therapeutic intervention leading to prevention.

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Li, Guanlin, Michael H. Cortez, Jonathan Dushoff, and Joshua S. Weitz. "When to be temperate: on the fitness benefits of lysis vs. lysogeny." Virus Evolution 6, no. 2 (May 22, 2020). http://dx.doi.org/10.1093/ve/veaa042.

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Abstract Bacterial viruses, that is ‘bacteriophage’ or ‘phage’, can infect and lyse their bacterial hosts, releasing new viral progeny. In addition to the lytic pathway, certain bacteriophage (i.e. ‘temperate’ bacteriophage) can also initiate lysogeny, a latent mode of infection in which the viral genome is integrated into and replicated with the bacterial chromosome. Subsequently, the integrated viral genome, that is the ‘prophage’, can induce and restart the lytic pathway. Here, we explore the relationship among infection mode, ecological context, and viral fitness, in essence asking: when should viruses be temperate? To do so, we use network loop analysis to quantify fitness in terms of network paths through the life history of an infectious pathogen that start and end with infected cells. This analysis reveals that temperate strategies, particularly those with direct benefits to cellular fitness, should be favored at low host abundances. This finding applies to a spectrum of mechanistic models of phage–bacteria dynamics spanning both explicit and implicit representations of intra-cellular infection dynamics. However, the same analysis reveals that temperate strategies, in and of themselves, do not provide an advantage when infection imposes a cost to cellular fitness. Hence, we use evolutionary invasion analysis to explore when temperate phage can invade microbial communities with circulating lytic phage. We find that lytic phage can drive down niche competition amongst microbial cells, facilitating the subsequent invasion of latent strategies that increase cellular resistance and/or immunity to infection by lytic viruses—notably this finding holds even when the prophage comes at a direct fitness cost to cellular reproduction. Altogether, our analysis identifies broad ecological conditions that favor latency and provide a principled framework for exploring the impacts of ecological context on both the short- and long-term benefits of being temperate.

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Arora, Srishtee, Xiqi Li, Andrew Hillhouse, Kranti Konganti, Sara V. Little, Sara D. Lawhon, David Threadgill, Samuel Shelburne, and Magnus Hook. "Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands." mBio 11, no. 1 (February 18, 2020). http://dx.doi.org/10.1128/mbio.02911-19.

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ABSTRACT Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCCmec) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB, and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR_B or DR_E. When inserted via DR_E, the sesJ gene was encoded in the SCC element. When inserted via DR_B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S. epidermidis clinical isolates. IMPORTANCE S. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis, is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections.

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Semenec, Lucie, Ismael A. Vergara, Andrew E. Laloo, Steve Petrovski, Philip L. Bond, and Ashley E. Franks. "Adaptive Evolution of Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa." mBio 11, no. 2 (April 7, 2020). http://dx.doi.org/10.1128/mbio.02875-19.

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ABSTRACT Interactions between microorganisms in mixed communities are highly complex, being either syntrophic, neutral, predatory, or competitive. Evolutionary changes can occur in the interaction dynamics between community members as they adapt to coexistence. Here, we report that the syntrophic interaction between Geobacter sulfurreducens and Pseudomonas aeruginosa coculture change in their dynamics over evolutionary time. Specifically, Geobacter sp. dominance increases with adaptation within the cocultures, as determined through quantitative PCR and fluorescence in situ hybridization. This suggests a transition from syntrophy to competition and demonstrates the rapid adaptive capacity of Geobacter spp. to dominate in cocultures with P. aeruginosa. Early in coculture establishment, two single-nucleotide variants in the G. sulfurreducens fabI and tetR genes emerged that were strongly selected for throughout coculture evolution with P. aeruginosa phenazine wild-type and phenazine-deficient mutants. Sequential window acquisition of all theoretical spectra-mass spectrometry (SWATH-MS) proteomics revealed that the tetR variant cooccurred with the upregulation of an adenylate cyclase transporter, CyaE, and a resistance-nodulation-division (RND) efflux pump notably known for antibiotic efflux. To determine whether antibiotic production was driving the increased expression of the multidrug efflux pump, we tested Pseudomonas-derived phenazine-1-carboxylic acid (PHZ-1-CA) for its potential to inhibit Geobacter growth and drive selection of the tetR and fabI genetic variants. Despite its inhibitory properties, PHZ-1-CA did not drive variant selection, indicating that other antibiotics may drive overexpression of the efflux pump and CyaE or that a novel role exists for these proteins in the context of this interaction. IMPORTANCE Geobacter and Pseudomonas spp. cohabit many of the same environments, where Geobacter spp. often dominate. Both bacteria are capable of extracellular electron transfer (EET) and play important roles in biogeochemical cycling. Although they recently in 2017 were demonstrated to undergo direct interspecies electron transfer (DIET) with one another, the genetic evolution of this syntrophic interaction has not been examined. Here, we use whole-genome sequencing of the cocultures before and after adaptive evolution to determine whether genetic selection is occurring. We also probe their interaction on a temporal level and determine whether their interaction dynamics change over the course of adaptive evolution. This study brings to light the multifaceted nature of interactions between just two microorganisms within a controlled environment and will aid in improving metabolic models of microbial communities comprising these two bacteria.

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Zhang, Si-Yu, Xiao Xiao, Song-Can Chen, Yong-Guan Zhu, Guo-Xin Sun, and Konstantinos T. Konstantinidis. "High arsenic levels increase activity rather than diversity or abundance of arsenic metabolism genes in paddy soils." Applied and Environmental Microbiology, August 11, 2021. http://dx.doi.org/10.1128/aem.01383-21.

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Arsenic (As) metabolism genes are generally present in soils but their diversity, relative abundance, and transcriptional activity in response to different As concentrations remain unclear, limiting our understanding of the microbial activities that control the fate of an important environmental pollutant. To address this issue, we applied metagenomics and metatranscriptomics to paddy soils showing a gradient of As concentrations to investigate As resistance genes ( ars ) including arsR , acr3 , arsB , arsC , arsM , arsI , arsP , and arsH as well as energy-generating As respiratory oxidation ( aioA ) and reduction ( arrA ) genes. Somewhat unexpectedly, the relative DNA abundances and diversity of ars , aioA , and arrA genes were not significantly different between low and high (∼10 vs ∼100 mg kg −1 ) As soils. By comparison to available metagenomes from other soils, geographic distance rather than As levels drove the different compositions of microbial communities. Arsenic significantly increased ars genes abundance only when its concentration was higher than 410 mg kg −1 . In contrast, between low and high As soils, metatranscriptomics revealed a significant increase in transcription of ars and aioA genes, which are induced by arsenite, the dominant As species in paddy soils, but not arrA genes, which are induced by arsenate. These patterns appeared to be community-wide as opposed to taxon-specific. Collectively, our findings advance understanding of how microbes respond to high As levels and the diversity of As metabolism genes in paddy soils and indicated that future studies of As metabolism in soil, or other environments, should include the function (transcriptome) level. IMPORTANCE Arsenic (As) is a toxic metalloid pervasively present in the environment. Microorganisms have evolved the capacity to metabolize As, and As metabolism genes are ubiquitously present in the environment even in the absence of high concentrations of As. However, these previous studies were carried out at the DNA level and thus, the activity of the As metabolism genes detected remains essentially speculative. Here, we show that the high As levels in paddy soils increased the transcriptional activity rather than the relative DNA abundance and diversity of As metabolism genes. These findings advance our understanding of how microbes respond to and cope with high As levels and have implications for better monitoring and managing an important toxic metalloid in agricultural soils and possibly other ecosystems.

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Kreamer, Naomi N., Flavia Costa, and Dianne K. Newman. "The Ferrous Iron-Responsive BqsRS Two-Component System Activates Genes That Promote Cationic Stress Tolerance." mBio 6, no. 2 (February 24, 2015). http://dx.doi.org/10.1128/mbio.02549-14.

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ABSTRACTThe physiological resistance of pathogens to antimicrobial treatment is a severe problem in the context of chronic infections. For example, the mucus-filled lungs of cystic fibrosis (CF) patients are readily colonized by diverse antibiotic-resistant microorganisms, includingPseudomonas aeruginosa. Previously, we showed that bioavailable ferrous iron [Fe(II)] is present in CF sputum at all stages of infection and constitutes a significant portion of the iron pool at advanced stages of lung function decline [R. C. Hunter et al., mBio 4(4):e00557-13, 2013].P. aeruginosa, a dominant CF pathogen, senses Fe(II) using a two-component signal transduction system, BqsRS, which is transcriptionally active in CF sputum [R. C. Hunter et al., mBio 4(4):e00557-13, 2013; N. N. Kreamer, J. C. Wilks, J. J. Marlow, M. L. Coleman, and D. K. Newman, J Bacteriol 194:1195–1204, 2012]. Here, we show that an RExxE motif in BqsS is required for BqsRS activation. Once Fe(II) is sensed, BqsR binds a tandem repeat DNA sequence, activating transcription. The BqsR regulon—defined through iterative bioinformatic predictions and experimental validation—includes several genes whose products are known to drive antibiotic resistance to aminoglycosides and polymyxins. Among them are genes encoding predicted determinants of polyamine transport and biosynthesis. Compared to the wild type,bqsSandbqsRdeletion mutants are sensitive to high levels of Fe(II), produce less spermidine in high Fe(II), and are more sensitive to tobramycin and polymyxin B but not arsenate, chromate, or cefsulodin. BqsRS thus mediates a physiological response to Fe(II) that guards the cell against positively charged molecules but not negatively charged stressors. These results suggest Fe(II) is an important environmental signal that, via BqsRS, bolsters tolerance of a variety of cationic stressors, including clinically important antimicrobial agents.IMPORTANCEClearing chronic infections is challenging due to the physiological resistance of opportunistic pathogens to antibiotics. Effective treatments are hindered by a lack of understanding of how these organisms survivein situ. Fe(II) is typically present at micromolar levels in soils and sedimentary habitats, as well as in CF sputum. All P. aeruginosa strains possess a two-component system, BqsRS, that specifically senses extracellular Fe(II) at low micromolar concentrations. Our work shows that BqsRS protects the cell against cationic perturbations to the cell envelope as well as low pH and reduction potential (Eh), conditions under which Fe2+is stable. Fe(II) can thus be understood as a proxy for a broader environmental state; the cellular response to its detection may help rationalize the resistance of P. aeruginosa to clinically important cationic antibiotics. This finding demonstrates the importance of considering environmental chemistry when exploring mechanisms of microbial survival in habitats that include the human body.

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Malviya, Manoj Nandlal, Sathiya Murthi, Ahmed A. Selim, Fadia Nazir Malik, Julet Mendoza, Dhanya Jayaraj, Vidya Ramdas, et al. "Neonatologist-Driven Antimicrobial Stewardship Program in a Neonatal Tertiary Care Center in Oman." American Journal of Perinatology, August 29, 2022. http://dx.doi.org/10.1055/a-1933-0104.

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Background The overuse of antimicrobials in neonates is not uncommon and has resulted in a global health crisis of antibiotic resistance. Objectives To evaluate changes associated with a neonatologist-driven antibiotic stewardship program (ASP) in antibiotics usage. Study design We conducted a pre-post retrospective cohort study in a tertiary care hospital in Oman. Neonates admitted in 2014-2015 were considered as the pre-ASP cohort. In 2016, a neonatologist-driven ASP was launched in the unit. The program included the optimization and standardization of antibiotics use for early and late-onset sepsis using the CDC's "broad principles," an advanced antimicrobial decision-support system to resolve contentious issues, and greater emphasis on education and behavior modification. Data from the years 2016-2019 were compared with previous data. The outcome of interest included days of therapy (DOT) for antimicrobials. Baseline characteristics and outcomes were compared using standard statistical measures. Results The study included 2098 neonates in the pre-ASP period and 5464 neonates in the post-ASP period. There was no difference in baseline characteristics. The antibiotic use decreased from 752 DOT per 1000 patient-days (PD) in the pre-ASP period to 264 DOT in the post-ASP period (64.8% reduction, P < 0.001). The proportion of neonates who received any antibiotics declined by 46% (pre-ASP = 1161/2098, post-ASP = 1676/5464). The most statistically significant reduction in DOT per 1000 PD was observed in the use of cefotaxime (82%), meropenem (74%), and piperacillin-tazobactam (74%). There was no change in mortality, culture-positive microbial profile, or MDRO incidence in the post-ASP period. Conclusions: Empowering frontline neonatologists to drive ASP was associated with a sustained reduction in antibiotics utilization.

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Sahu, Kuleshwar Prasad, A. Kumar, K. Sakthivel, Bhaskar Reddy, Mukesh Kumar, Asharani Patel, Neelam Sheoran, et al. "Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease." Environmental Microbiome 17, no. 1 (May 26, 2022). http://dx.doi.org/10.1186/s40793-022-00421-5.

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Abstract Background With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future. Results The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate ‘Mountain Zone’ on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings. Conclusions PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future. Graphical abstract

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